Single-stranded RNAi agents containing an internal, non-nucleic acid spacer

ABSTRACT

The instant disclosure features single-stranded RNA molecules comprising one or more internal, non-nucleotide spacers. A non-nucleotide spacer covalently links nucleotide portions of the molecule. The single-stranded RNA molecules function as guide or antisense strands that are capable of inhibiting gene expression via an RNA interference mechanism and, thus, represent single-stranded RNAi agents. The single-stranded RNAi molecules can be used in methods for a variety of therapeutic, diagnostic, target validation, genomic discovery, genetic engineering, and pharmacogenomic applications.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No. 14/967,974, filed Dec. 14, 2015, which is a continuation of U.S. patent application Ser. No. 13/818,306, filed Aug. 19, 2011, now U.S. Pat. No. 9,243,246, issued Jan. 26, 2016, which is a National Stage Entry of PCT Application No. PCT/US2011/048338, filed Aug. 19, 2011 which claims the benefit of U.S. Provisional Application No. 61/376,471, filed Aug. 24, 2010. Each of these prior applications is incorporated herein by reference in its entirety.

BACKGROUND OF THE INVENTION

The RNA interference (RNAi) pathway is an evolutionarily conserved mode of gene regulation. The RNAi process is initiated by double-stranded RNA (dsRNA) produced from various exogenous or endogenous sources (e.g., experimental introduction, viral infection). The dsRNA is cleaved by Dicer to generate 20-25 nucleotide small-interfering RNA (siRNA) duplexes. These duplexes are then loaded onto the RNA-induced silencing complex (RISC), and before RISC is activated, the passenger/sense strand of the duplex is removed. The single guide/antisense strand remains associated with RISC and directs cleavage of the target mRNA. Thus, duplexed siRNA have become an important tool for both research and nucleic acid-based therapeutics.

RNAi gene silencing can occur via single-stranded or double-stranded RNA molecules. In the last ten years, it has been reported that single-stranded antisense siRNA are almost as potent as the siRNA duplex (see, e.g., Schwarz et al., 2002, Mol. Cell. 10:537-548; Martinez et al., 2002, Cell 110:563-574; Amarzguioui et al., 2003, Nucleic Acids Res. 31:589-595; and Holen et al., 2003, Nucleic Acids Res. 31:2401-2407). There are benefits in utilizing single-stranded RNA molecules, as opposed to duplexed versions, for gene silencing. Their lower molecule weight may make them easier to cross cell membranes. Single-stranded RNA molecules are also half the mass and volume of duplexed siRNA, implicating a manufacturing cost advantage. Thus, there remains a heightened interest in formulating new and advantageous design features suitable for single-stranded RNAi molecules.

SUMMARY OF THE INVENTION

The instant disclosure provides single-stranded RNA molecules which comprise: (a) a nucleic acid portion comprising two or more nucleotide portions, and (b) an internal (as opposed to “terminal”) spacer portion comprising one or more non-nucleotide spacer portions, wherein a non-nucleotide spacer portion covalently links two nucleotide portions of the molecule. The nucleotide portions of the single-stranded RNA molecules of the invention are not complementary to each other and, thus, said portions do not form base pairs. The single-stranded RNA molecules of the invention function as guide or antisense strands that are capable of inhibiting gene expression via an RNA interference mechanism and, thus, represent single-stranded RNAi agents.

A single-stranded RNAi molecule of the invention has a single-stranded oligonucleotide structure and mediates RNA interference against a target RNA. A single-stranded RNAi molecule comprises: (a) a nucleic acid portion comprising a first nucleotide portion (N1) and a second nucleotide portion (N2), wherein said nucleic acid portion comprises at least 8 nucleotides that can base pair with a target RNA, and wherein the total number of nucleotides within the nucleic acid portion is from 8 to 26 nucleotides; and, (b) an internal spacer portion comprising at least a first non-nucleotide spacer portion (S1) that covalently links the first and second nucleotide portions. The first and second nucleotide portions are not self complementary. The total number of nucleotides of a single-stranded RNAi molecule of the invention (e.g., 8 to 26) is distributed between the nucleotide portions of the molecule, wherein each nucleotide portion contains at least one nucleotide.

In one embodiment, the nucleic acid portion of a single-stranded RNAi molecule of the invention contains two nucleotide portions, referred to as the first nucleotide portion (N1) and the second nucleotide portion (N2). The first and second nucleotide portions of an RNAi molecule of the invention are covalently attached to a non-nucleotide spacer portion of the molecule. In another embodiment, the nucleic acid portion of a single-stranded RNAi molecule of the invention contains more than one nucleotide portion (e.g., 3, 4, or 5, referred to as third (N3), fourth (N4) or fifth (N5) nucleotide portions, respectively).

In one embodiment, the internal spacer portion of a single-stranded RNAi molecule of the invention contains only one non-nucleotide spacer portion, referred to as the first non-nucleotide spacer portion (S1). The first non-nucleotide spacer portion (S1) of an RNAi molecule of the invention is covalently attached to two nucleotides and/or non-nucleotide substitutes, each located within a distinct nucleotide portion of the single-stranded molecule. In another embodiment, the internal spacer portion of a single-stranded RNAi molecule of the invention contains more than one non-nucleotide spacer portion (e.g., 2, 3, or 4, referred to as second (S2), third (S3) or fourth (S4) non-nucleotide spacer portions, respectively).

A single-stranded RNAi molecule of the invention comprises a nucleotide sequence that is partially, substantially or perfectly complementary to an RNA target site in a cell.

In one embodiment, a single-stranded RNAi molecule of the invention comprises a nucleotide sequence that is partially, substantially, or perfectly homologous to the guide strand of a naturally-occurring miRNA and, thus, functions as a miRNA mimetic. A single-stranded miRNA mimetic of the invention is designed based on a corresponding, naturally-occurring miRNA, wherein at least one non-nucleotide spacer portion is either located between two adjacent nucleotides of the naturally-occurring miRNA guide strand sequence or substituted for from one to about 12 internal (i.e., non-terminal) nucleotides of the naturally-occurring miRNA guide strand sequence.

In another embodiment, a single-stranded RNAi molecule of the invention is an analog of either a single-stranded siRNA or the guide/antisense strand of a duplex siRNA, wherein the single-stranded RNAi molecule comprises a sequence that is partially, substantially, or perfectly homologous to the corresponding single-stranded siRNA or the guide strand of the corresponding duplex siRNA. The corresponding single-stranded siRNA or duplex siRNA may be known to inhibit gene expression via an RNAi mechanism. In this embodiment, the single-stranded RNAi molecule represents a single-stranded siRNA mimetic. A single-stranded siRNA mimetic of the invention is designed based on a corresponding siRNA, wherein at least one non-nucleotide spacer portion is either located between two adjacent nucleotides of the siRNA guide strand sequence or substituted for from one to about 4 nucleotides of the corresponding siRNA guide strand sequence.

A single-stranded RNAi molecule of the invention can comprise substitutions, chemically-modified nucleotides, and non-nucleotides, including substitutions or modifications in the backbone, sugars, bases, or nucleosides. In certain embodiments, the use of substituted or modified single-stranded RNAi molecules of this disclosure can enable achievement of a given therapeutic effect at a lower dose since these molecules may be designed to have an increased half-life in a subject or biological samples (e.g., serum). Furthermore, certain substitutions or modifications can be used to improve the bioavailability of single-stranded RNAi molecules by targeting particular cells or tissues or improving cellular uptake of the single-stranded RNAi molecules.

The internal spacer portion of a single-stranded RNAi molecule of the invention can comprise one or more non-nucleotide spacer portions. A non-nucleotide spacer portion can include any aliphatic or aromatic chemical group that can be further substituted, wherein said spacer portion does not contain a nucleotide. The spacer portion can be substituted with a chemical moiety that provides additional functionality to a single-stranded RNAi molecule. For example, a non-nucleotide spacer portion can be substituted with a moiety that binds specifically to a target molecule of interest or facilitates/enhances cellular delivery of the molecule. In one embodiment of the invention, a non-nucleotide spacer portion includes an alkyl, alkenyl or alkynyl chain of preferably 1 to 20 carbons that can be optionally substituted.

The single-stranded RNAi molecules of the invention are useful reagents, which can be used in methods for a variety of therapeutic, diagnostic, target validation, genomic discovery, genetic engineering, and pharmacogenomic applications. Thus, the prevent invention further includes compositions comprising a single-stranded RNAi molecule of the disclosure and methods for inhibiting expression of one or more corresponding target mRNAs in a cell or organism. This disclosure provides methods and single-stranded RNAi molecule compositions for treating a subject, including a human cell, tissue or individual.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the degree of inhibition of VAMP3 target expression by single-stranded miR-124 analogs containing a C3 spacer using a RT-qPCR assay. The structure and sequence of the analogs are specifically described in Table 2, infra. In the schematic drawings of the miR-124 analogs, the circles represent nucleotides, with the exception of the black circle located at the 5′ terminus which represents a 5′ phosphate. The open circles represent 2′-deoxy-2′-fluoro nucleotides. The black circles located at the 3′ terminus of the schematics represent 2′-O-methyl nucleotides, and the “3” represents the location of the C3 spacer. In the schematic of the “124(21)-8p-16rrr” analog, the three internal black circles represent unmodified ribonucleotides. The longer bars in the graph indicate greater knockdown, and duplicate bars indicate biological replicates.

FIG. 2 shows the degree of inhibition of VAMP3 target expression by single-stranded miR-124 analogs containing a C6 spacer using a RT-qPCR assay. The structure and sequence of the analogs are specifically described in Table 2, infra. In the schematic drawings of the miR-124 analogs, the circles represent nucleotides, with the exception of the black circle located at the 5′ terminus which represents a 5′ phosphate. The open circles represent 2′-deoxy-2′-fluoro nucleotides. The black circles located at the 3′ terminus of the schematics represent 2′-O-methyl nucleotides, and the “6” represents the location of the C6 spacer. In the schematic of the “124(21)-8p-16rrr” analog, the three internal black circles represent unmodified ribonucleotides. The longer bars in the graph indicate greater knockdown, and duplicate bars indicate biological replicates.

FIG. 3 shows the dose-dependent response of VAMP3 expression for a subset of the analogs tested in FIGS. 1 and 2. VAMP3 expression is depicted along the y-axis. The dose of the miR-124 analog tested (see Table 2, infra, for structure and sequences) is depicted along the x-axis, ranging from the lowest doses on the left to the highest doses on the right.

FIG. 4 shows the degree of inhibition by single-stranded miR-124 analogs containing a C3 spacer using a reporter assay that measures knockdown of a co-transfected luciferase reporter that carries two target sites matching the seed region of miR-124. The structure and sequence of the analogs are specifically described in Table 2, infra. In the schematic drawings of the miR-124 analogs, the circles represent nucleotides, with the exception of the black circle located at the 5′ terminus which represents a 5′ phosphate. The open circles represent 2′-deoxy-2′-fluoro nucleotides. The black circles located at the 3′ terminus of the schematics represent 2′-O-methyl nucleotides, and the “3” represents the location of the C3 spacer. In the schematic of the “124(21)-8p-16rrr” analog, the three internal black circles represent unmodified ribonucleotides. The duplicate bars of the graph indicate biological replicates, and longer bars indicate greater inhibition.

FIG. 5 shows the degree of inhibition by single-stranded miR-124 analogs containing a C6 spacer using a reporter assay that measures knockdown of a co-transfected luciferase reporter that carries two target sites matching the seed region of miR-124. The structure and sequence of the analogs are specifically described in Table 2, infra. In the schematic drawings of the miR-124 analogs, the circles represent nucleotides, with the exception of the black circle located at the 5′ terminus which represents a 5′ phosphate. The open circles represent 2′-deoxy-2′-fluoro nucleotides. The black circles located at the 3′ terminus of the schematics represent 2′-O-methyl nucleotides, and the “6” represents the location of the C6 spacer. In the schematic of the “124(21)-8p-16rrr” analog, the three internal black circles represent unmodified ribonucleotides. The duplicate bars indicate biological replicates, and longer bars indicate greater inhibition.

FIGS. 6A and 6B show the dose-dependent response of target expression inhibition of two different luciferase reporters for a subset of the single-stranded miR-124 analogs tested in FIG. 3. In FIG. 6A, the inhibition activity shown is against a luciferase reporter with two matches to the miR-124 seed region, representing the miRNA activity of the tested analogs. In FIG. 6B, the inhibition activity shown is against a luciferase reporter with two full-length matches to miR-124, representing the siRNA activity of the tested analogs.

FIG. 7 compares the knockdown of ApoB mRNA using ApoB-targeted single stranded (guide strand) oligonucleotides having a C3 spacer incorporated at either position 15 (“485 c3@pos15”), 16 (“485 c3@pos16”), 17 (“485 c3@pos17”), 18 (“485 c3@pos185”), or 19 (“485 c3@pos19”) (relative to the 5′ of the oligo) to the corresponding single stranded oligonucleotide without the spacer (“485”) at two different concentrations (100 nM and 10 nM). All of the single stranded molecules are composed of 2′-deoxy-2′-fluoro nucleotides at both pyrimidine and purine nucleotides, a 5′ phosphate, and two 2′-O-methyl nucleotides at the 3′ terminus.

FIGS. 8 and 9 compares ApoB mRNA knockdown using 30 different single strand sequences targeting ApoB with C3 spacer at either position 18 (FIG. 8) or position 19 (FIG. 9) at two concentrations (100 nM and 10 nM). Single strands are notated on the x-axis by the position within the ApoB mRNA which they target. All of the single stranded molecules are composed of 2′-deoxy-2′-fluoro nucleotides at both pyrimidine and purine nucleotides, a 5′ phosphate, and two 2′-O-methyl nucleotides at the 3′ terminus.

FIG. 10 compares ApoB mRNA knockdown at 100 nM concentration using single stranded molecules targeting each of the 30 different ApoB target sites tested in FIGS. 8 and 9—single strands without a C3 spacer (“all-flu-p”), with a C3 spacer at position 18 (“all-flu-c3-18-p”), and with a C3 spacer at position 19 (“all-flu-c3-19-p”). All of the single stranded molecules are composed of 2′-deoxy-2′-fluoro nucleotides at both pyrimidine and purine nucleotides, a 5′ phosphate, and two 2′-O-methyl nucleotides at the 3′ terminus.

DETAILED DESCRIPTION OF THE INVENTION A. Terms and Definitions

The following terminology and definitions apply as used in the present application.

As used in this specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the content clearly dictates otherwise. Thus, for example, reference to “a cell” includes a combination of two or more cells, and the like.

Any concentration range, percentage range, ratio range, or integer range is to be understood to include the value of any integer within the recited range, and when appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise indicated.

“About” or “approximately,” as used herein, in reference to a number are generally taken to include numbers that fall within a range of 5% in either direction (greater than or less than) of the number unless otherwise stated or otherwise evident from the context (except where such number would exceed 100% of a possible value). Where ranges are stated, the endpoints are included within the range unless otherwise stated or otherwise evident from the context.

As used herein, the terms “including” (and any form thereof, such as “includes” and “include), “comprising” (and any form thereof, such as “comprise” and “comprises”), “having” (and any form thereof, such as “has” or “have”), or “containing” (and any form thereof, such as “contains” or “contain”) are inclusive and open-ended and do not exclude additional, un-recited elements or method steps.

“Analog” as used herein refers to its meaning as is generally accepted in the art. The term generally refers to a compound or molecule that is structurally similar to a parent compound or molecule (e.g., a nucleotide, a naturally-occurring miRNA), but differs slightly in composition (e.g., one atom or functional group is different, added, or removed). The analog may or may not have different chemical or physical properties than the original parent compound or molecule and may or may not have improved biological or chemical activity. For example, the analog may be more hydrophilic or it may have altered activity of the parent compound/molecule. The analog may be a naturally or non-naturally occurring (e.g., chemically-modified or recombinant) variant of the original parent compound/molecule. An example of an RNA analog is an RNA molecule comprising a nucleotide analog. A nucleotide analog is a nucleotide that is chemically-modified at the sugar, base or nucleoside, as is generally recognized in the art.

As used herein, the term “mimetic” refers to its meaning as is generally accepted in the art. The term generally refers to a molecule that is structurally different from a reference molecule. For example, a reference molecule for purposes of certain embodiments of the present invention can be a naturally-occurring miRNA molecule, or a single-stranded siRNA molecule, that does not contain a non-nucleotide internal spacer. The mimetic is capable of performing one or more or all of the biological, physiological, and/or chemical functions that are within the capabilities of the reference molecule. The mimetic and the reference molecule do not have to be functional equivalents, but the mimetic should be able to perform one or more functions and exhibit at least 5% or more, 10% or more, 20% or more, 30% or more, 40% or more, 50% or more, 60% or more, 70% or more, 80% or more, or 90% or more of the activity of the reference molecule, as measured and compared using assays or parameters that are suitable to represent the shared function(s). The terms “analog” and “mimetic,” when describing an RNAi molecule of the disclosure that is structurally different from a reference RNAi molecule, can be used interchangeably.

The term “nucleotide” refers to its meaning as is generally recognized in the art. Nucleotides generally comprise a nucleobase, a sugar, and an internucleoside linkage, e.g., a phosphate. The base can be a natural base (standard), a modified base, or a base analog, as are well known in the art. Such bases are generally located at the 1′ position of a nucleotide sugar moiety. Additionally, the nucleotides can be unmodified or modified at the sugar, internucleoside linkage, and/or base moiety (also referred to interchangeably as nucleotide analogs, modified nucleotides, non-natural nucleotides, and non-standard nucleotides); see, for example, U.S. application Ser. No. 12/064,014.

The terms “polynucleotide” and “oligonucleotide” as used herein refer to the meaning as is generally accepted in the art. The terms generally refer to a chain of nucleotides. “Nucleic acids” and “nucleic acid molecules” are polymers of nucleotides. Thus, “nucleic acids,” “polynucleotides” and “oligonucleotides” are interchangeable herein. One skilled in the art has the general knowledge that nucleic acids are polynucleotides which can be hydrolyzed into monomeric nucleotides. Monomeric nucleotides can be further hydrolyzed into nucleosides.

By “a contiguous stretch of nucleotides” is meant a continuous series of at least 2 nucleotides. The bonds connecting the nucleotides within the stretch are phosphodiester bonds.

The term “RNA” as used herein refers to its meaning as is generally accepted in the art. The term generally refers to a molecule comprising at least one ribofuranoside residue, such as a ribonucleotide. The term “ribonucleotide” means a nucleotide with a hydroxyl group at the 2′ position of a β-D-ribofuranose moiety. The term refers to a double-stranded RNA, a single-stranded RNA, an isolated RNA such as a partially purified RNA, an essentially pure RNA, a synthetic RNA, a recombinantly-produced RNA, or an altered RNA that differs from a naturally-occurring RNA by the addition, deletion, substitution and/or alteration of one or more nucleotides therein. Such alterations can include addition of non-nucleotide material, for example, at one or more non-terminal nucleotides of an RNA molecule. As such, nucleotides in the single-stranded RNA molecules of the invention can comprise non-standard nucleotides, such as non-naturally occurring nucleotides, chemically-synthesized and/or modified nucleotides, or deoxynucleotides. The altered RNA is referred to as a “modified RNA” or a “RNA analog.”

The term “pyrimidine” as used herein refers to its meaning as is generally accepted in the art. The term generally refers to conventional pyrimidine bases, including the standard pyrimidine bases uracil, thymidine, and cytosine. In addition, the term pyrimidine is contemplated to embrace non-standard pyrimidine bases or acids, such as 5-methyluracil, 2-thio-5-methyluracil, 4-thiouracil, pseudouracil, dihydrouracil, orotate, 5-methylcytosine, or the like, as well as a chemically-modified bases or “universal bases,” which can be used to substitute for a standard pyrimidine within the nucleic acid molecules of this disclosure.

The term “purine” as used herein refers to its meaning as is generally accepted in the art. The term generally refers to conventional purine bases, including the standard purine bases adenine and guanine. In addition, the term “purine” is contemplated to embrace non-standard purine bases or acids, such as N₂-methylguanine, inosine, diaminopurine and the like, as well as chemically-modified bases or “universal bases,” which can be used to substitute for standard purines herein.

As described herein, a “base pair” can be formed between two nucleotides, a nucleotide and a modified nucleotide, two modified nucleotides, a nucleotide and a nucleotide analog, two nucleotide analogs, a nucleotide and a non-nucleotide substitute moiety, or two non-nucleotide substitute moieties. In a specific embodiment, a non-nucleotide substitute can comprise any chemical moiety that is capable of associating with a component of the cellular RNAi machinery, such as, for example, the PAZ domain, the PIWI domain, and/or other Argonaute protein domains associated with the RISC. Non-traditional Watson-Crick base pairs are also understood as “non-canonical base pairs,” which is meant any non-Watson Crick base pair, such as mismatches and/or wobble base pairs, including flipped mismatches, single hydrogen bond mismatches, trans-type mismatches, triple base interactions, and quadruple base interactions. Non-limiting examples of such non-canonical base pairs include, but are not limited to, AC reverse Hoogsteen, AC wobble, AU reverse Hoogsteen, GU wobble, AA N7 amino, CC 2-carbonyl-amino(H1)-N3-amino(H2), GA sheared, UC 4-carbonyl-amino, UU imino-carbonyl, AC reverse wobble, AU Hoogsteen, AU reverse Watson Crick, CG reverse Watson Crick, GC N3-amino-amino N3, AA N1-amino symmetric, AA N7-amino symmetric, GA N7-N1 amino-carbonyl, GA+carbonyl-amino N7-N1, GG N1-carbonyl symmetric, GG N3-amino symmetric, CC carbonyl-amino symmetric, CC N3-amino symmetric, UU 2-carbonyl-imino symmetric, UU 4-carbonyl-imino symmetric, AA amino-N3, AA N1-amino, AC amino 2-carbonyl, AC N3-amino, AC N7-amino, AU amino-4-carbonyl, AU N1-imino, AU N3-imino, AU N7-imino, CC carbonyl-amino, GA amino-N1, GA amino-N7, GA carbonyl-amino, GA N3-amino, GC amino-N3, GC carbonyl-amino, GC N3-amino, GC N7-amino, GG amino-N7, GG carbonyl-imino, GG N7-amino, GU amino-2-carbonyl, GU carbonyl-imino, GU imino-2-carbonyl, GU N7-imino, psiU imino-2-carbonyl, UC 4-carbonyl-amino, UC imino-carbonyl, UU imino-4-carbonyl, AC C2-H—N3, GA carbonyl-C2-H, UU imino-4-carbonyl 2 carbonyl-C5-H, AC amino(A) N3(C)-carbonyl, GC imino amino-carbonyl, Gpsi imino-2-carbonyl amino-2-carbonyl, and GU imino amino-2-carbonyl base pairs.

As used herein, the term “complementary” (or “complementarity”) refers to its meaning as is generally accepted in the art. The term generally refers to the formation or existence of hydrogen bond(s) between one nucleic acid sequence and another nucleic acid sequence by either traditional Watson-Crick or other non-traditional types of bonds as described herein. With reference to exemplary nucleic acid molecules of the invention, complementarity can be found between a single-stranded RNAi of the invention and an RNA target sequence. The binding free energy for a nucleic acid molecule with its complementary sequence is sufficient to allow the relevant function of the nucleic acid to proceed, e.g., RNAi activity. Determination of binding free energies for nucleic acid molecules is well known in the art (see, e.g., Turner et al., 1987, CSH Symp. Quant. Biol. LII pp. 123-133; Frier et al., 1986, Proc. Nat. Acad. Sci. USA 83:9373-9377; Turner et al., 1987, J. Am. Chem. Soc. 109:3783-3785).

As used herein, the term “perfectly complementary” (or “perfect complementarity”) between a first nucleic acid molecule (e.g., a single-stranded RNAi molecule of the present invention) and the second nucleic acid molecule (e.g., a target RNA sequence) means that all the contiguous residues of the first nucleic acid sequence will hydrogen bond with the same number of contiguous residues in the second nucleic acid sequence. For example, two or more perfectly complementary nucleic acid strands can have the same number of nucleotides (i.e., have the same length and form one double-stranded region with or without an overhang), or have a different number of nucleotides (e.g., one strand may be shorter but fully contained within a second strand). As an example, if a single-stranded RNAi molecule of the invention has a first nucleotide portion of only 1 nucleotide and a second nucleotide portion of 10 contiguous nucleotides, wherein all of the 10 nucleotides in the second nucleotide portion of the molecule base pair with the RNA target sequence, the RNAi molecule is perfectly complementary with the RNA target sequence. The single nucleotide included in the first nucleotide portion is not included when determining the degree of complementarity because it is not within a contiguous chain of nucleotides. However, in this example, if the first nucleotide portion contains 2 nucleotides, the RNAi molecule is perfectly complementary to the RNA target sequence if the 2 nucleotides of the first nucleotide portion and the 10 nucleotides of the second nucleotide portion base pair with the RNA target sequence.

Complementary nucleic acid molecules may have wrongly paired bases—that is, bases that cannot form a traditional Watson-Crick base pair (i.e., forming a hydrogen bond) or other non-traditional types of base pair (i.e., “mismatched” bases, formed or held together by non-traditional forces that are not hydrogen bonds). The term “partially complementary” (or “partial complementarity”) between a first nucleic acid molecule (e.g., a single-stranded RNAi molecule of the present invention) and second nucleic acid molecule (e.g., a target RNA sequence) indicates that various mismatches or non-based paired nucleotides (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more mismatches or non-based paired nucleotides) occur between the nucleotide sequences, which can result in, for example, in bulges or loops. Such partial complementarity can be represented by a percent (%) complementarity that is determined by the number of base paired nucleotides in relation to the total number of nucleotides involved, e.g., about 50%, 60%, 70%, 80%, 90% etc. For example, a first nucleic acid molecule may have 10 nucleotides and a second nucleic acid molecule may have 10 nucleotides, then base pairing of 5, 6, 7, 8, 9, or 10 nucleotides between the first and second nucleic acid molecules, which may or may not form a contiguous double-stranded region, represents 50%, 60%, 70%, 80%, 90%, or 100% complementarity, respectively. In relation to the present invention, such partial complementarity is permitted to the extent that a single-stranded RNAi molecule of the invention maintains its function, for example the ability to mediate sequence specific RNAi.

A first nucleic acid molecule can be “substantially complementary” to a second nucleic acid. By “substantially complementary” it is meant that a first nucleic acid sequence (e.g., a single-stranded RNAi molecule of the present invention) is at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% complementary to a second nucleic acid sequence (e.g., a RNA target sequence). As used herein, a first nucleic acid molecule can be both “partially complementary” and “substantially complementary” to a second nucleic acid molecule.

As used herein, the term “homologous” (or “homology”) refers to its meaning as is generally accepted in the art. The term generally refers to the number of nucleotides of the subject nucleic acid sequence that has been matched to identical nucleotides of a reference nucleic acid sequence, typically as determined by a sequence analysis program (e.g., Karlin and Altschul, 1990, PNAS 87:2264-2268; Karlin and Altschul, 1993, PNAS 90:5873-5877) or by visual inspection. The term “perfect homology” (or “perfectly homologous”) as used herein refers to complete (100%) homology or “identity” between a reference sequence and a subject nucleic acid sequence. As used herein, the term “substantially homologous” (or “substantial homology”) is meant that the subject sequence shares at least 50% (e.g., at least 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99%) homologous nucleotides with the nucleotides of the same nucleotide positions in a reference sequence.

The phrase “chemical modification” as used herein refers to its meaning as is generally accepted in the art. With reference to exemplary nucleic acid molecules of the invention, the term refers to any modification of the chemical structure of the nucleotides that differs from nucleotides of native RNA. The term “chemical modification” encompasses the addition, substitution, or modification of native RNA at the sugar, base, or internucleotide linkage, as described herein or as is otherwise known in the art. In certain embodiments, the term “chemical modification” can refer to certain forms of RNA that are naturally-occurring in certain biological systems, for example 2′-O-methyl modifications or inosine modifications.

The phrase “modified nucleotide” as used herein refers to its meaning as is generally accepted in the art. The term generally refers a nucleotide that contains a modification in the chemical structure of the base, sugar and/or phosphate of the unmodified (or natural) nucleotide, as is generally known in the art. Non-limiting examples of modified nucleotides are described herein and in U.S. application Ser. No. 12/064,014.

“Percent modification” refers to its meaning as is generally accepted in the art. As used herein, the term generally refers to the number of nucleotides in a single-stranded RNA molecule of the invention that have been modified. The extent of chemical modifications will depend upon various factors well known to one skilled in the art (e.g., target RNA, off-target silencing, degree of endonuclease degradation).

The term “phosphorothioate” refers to its meaning as is generally accepted in the art. The term generally refers to an internucleotide phosphate linkage comprising one or more sulfur atoms in place of an oxygen atom. Hence, the term phosphorothioate refers to both phosphorothioate and phosphorodithioate internucleotide linkages.

As used herein, the term “locked nucleic acid” (LNA) has the structure of the general Formula I:

X and Y are independently selected from the group consisting of —O—, —S—, —N(H)—, —N(R)—, —CH₂—, or —CH— (if part of a double bond), —CH₂—O—, CH₂—S—, CH₂—N(H)—, —CH₂—N(R)—, —CH₂—CH₂—, and CH₂—CH— (if part of a double bond), —CH═CH—, where R is selected from hydrogen and C₁₋₄-alkyl; Z and Z* are independently selected from an internucleotide linkage, a terminal group or a protecting group; B constitutes a natural or non-natural nucleobase; and the asymmetric groups may be found in either orientation.

The four chiral centers of Formula I, as shown, are in a fixed configuration, but their configurations are not necessary fixed. As such, the chiral centers can be found in different configurations, such as those represented in Formula II (below). Thus, each chiral center in Formula 1 can exist in either R or S configuration. The definition of R (rectus) and S (sininster) are described in the IUPAC 1974 Recommendations, Section E, Fundamental Stereochemistry: The rules can be found in Pure Appl. Chem. 45, 13-30 (1976) and In “Nomenclature of Organic Chemistry” Pergamon, New York, 1979.

The terminal groups are selected independently among from hydrogen, azido, halogen, cyano, nitro, hydroxy, Prot-O—, Act-O—, mercapto, Prot-S—, Act-S—, C₁₋₆-alkylthio, amino, Prot-N(R^(H))—, Act-N(R^(H))—, mono- or di(C₁₋₆-alkyl)amino, optionally substituted C₁₋₆-alkoxy, optionally substituted C₁₋₆-alkyl, optionally substituted C₂₋₆-alkenyl, optionally substituted C₂₋₆-alkenyloxy, optionally substituted C₂₋₆-alkynyl, optionally substituted C₂₋₆-alkynyloxy, monophosphate, monothiophosphate, diphosphate, dithiophosphate triphosphate, trithiophosphate, DNA intercalators, photochemically active groups, thermochemically active groups, chelating groups, reporter groups, ligands, carboxy, sulphono, hydroxymethyl, Prot-O—CH₂—, Act-O—CH₂—, aminomethyl, Prot-N(R^(H))—CH₂—, Act-N(R^(H))—CH₂—, carboxy methyl, sulphonomethyl, where Prot is a protection group for —OH, —SH, and —NH(R^(H)), respectively, Act is an activation group for —OH, —SH, and —NH(R^(H)), respectively, and R^(H) is selected from hydrogen and C₁₋₆-alkyl.

The protection groups of hydroxy substituents comprises substituted trityl, such as 4,4′-dimethoxytrityloxy (DMT), 4-monomethoxytrityloxy (MMT), and trityloxy, optionally substituted 9-(9-phenyl)xanthenyloxy (pixyl), optionally substituted methoxytetrahydropyranyloxy (mthp), silyloxy such as trimethylsilyloxy (TMS), triisopropylsilyloxy (TIPS)₇ tert-butyldimethylsilyloxy (TBDMS), triethylsilyloxy, and phenyldimethylsilyloxy, tert-butylethers, acetals (including two hydroxy groups), acyloxy such as acetyl or halogen substituted acetyls.

“Act” designates an activation group for —OH, —SH, and —NH(R^(H)), respectively. Such activation groups are, for example, selected from optionally substituted O-phosphoramidite, optionally substituted O-phosphortriester, optionally substituted O-phosphordiester, optionally substituted H-phosphonate, and optionally substituted O-phosphonate.

B constitutes a natural or non-natural nucleobase and selected among adenine, cytosine, 5-methylcytosine, isocytosine, pseudoisocytosine, guanine, thymine, uracil, 5-bromouracil, 5-propynyluracil, 5-propyny-6-fluoroluracil, 5-methylthiazoleuracil, 6-aminopurine, 2-aminopurine, inosine, diaminopurine, 7-propyne-7-deazaadenine, 7-propyne-7-deazaguanine, and 2-chloro-6-aminopurine.

Preferably, the locked nucleic acid (LNA) used in a single-stranded RNAi molecule of the invention comprises a LNA structure according to any of the Formulas II:

wherein Y is —O—, —S—, —NH—, or N(R^(H)); Z and Z* are independently selected among an internucleotide linkage, a terminal group or a protecting group; and B constitutes a natural or non-natural nucleobase. These exemplary LNA monomers and others, as well as their preparation are described in WO 99/14226 and subsequent applications, WO 00/56746, WO 00/56748, WO 00/66604, WO 00/125248, WO 02/28875, WO 2002/094250 and WO 2003/006475; the disclosure of all of which are incorporated herein by reference.

The term “universal base” refers to its meaning as is generally accepted in the art. The term generally refers to nucleotide base analogs that form base pairs with each of the standard DNA/RNA bases with little discrimination among them, and is recognized by intracellular enzymes. See, e.g., Loakes et al., 1997, J. Mol. Bio. 270:426-435. Non-limiting examples of universal bases include C-phenyl, C-naphthyl and other aromatic derivatives, inosine, azole carbozamides, and nitroazole derivatives such as 3′-nitropyrrole, 4-nitroindole, 5-nitroindole, and 6-nitroindole as known in the art. See, e.g., Loakes, 2001, Nucleic Acids Res. 29:2437.

As used herein, the phrase “RNA interference” (also called “RNAi” herein) refers to its meaning as is generally accepted in the art. The term generally refers to the biological process of inhibiting, decreasing, or down-regulating gene expression in a cell, and which is mediated by short interfering nucleic acid molecules (e.g., siRNAs, miRNAs, shRNAs), see for example Zamore and Haley, 2005, Science 309:1519-1524; Vaughn and Martienssen, 2005, Science 309:1525-1526; Zamore et al., 2000, Cell 101:25-33; Bass, 2001, Nature 411:428-429; Elbashir et al., 2001, Nature 411:494-498; and Kreutzer et al., International PCT Publication No. WO 00/44895; Zernicka-Goetz et al., International PCT Publication No. WO 01/36646; Fire, International PCT Publication No. WO 99/32619; Plaetinck et al., International PCT Publication No. WO 00/01846; Mello and Fire, International PCT Publication No. WO 01/29058; Deschamps-Depaillette, International PCT Publication No. WO 99/07409; and Li et al., International PCT Publication No. WO 00/44914; Allshire, 2002, Science 297:1818-1819; Volpe et al., 2002, Science 297:1833-1837; Jenuwein, 2002, Science 297:2215-2218; and Hall et al., 2002, Science 297:2232-2237; Hutvagner and Zamore, 2002, Science 297:2056-60; McManus et al., 2002, RNA 8:842-850; Reinhart et al., 2002, Gene & Dev. 16:1616-1626; and Reinhart & Bartel, 2002, Science 297:1831). Additionally, the term “RNA interference” (or “RNAi”) is meant to be equivalent to other terms used to describe sequence-specific RNA interference, such as post-transcriptional gene silencing, translational inhibition, transcriptional inhibition, or epigenetics. For example, single-stranded RNA molecules of the invention can be used to epigenetically silence genes at either the post-transcriptional level or the pre-transcriptional level. In a non-limiting example, epigenetic modulation of gene expression by single-stranded RNA molecules of the invention can result from modification of chromatin structure or methylation patterns to alter gene expression (see, for example, Verdel et al., 2004, Science 303:672-676; Pal-Bhadra et al., 2004, Science 303:669-672; Allshire, 2002, Science 297:1818-1819; Volpe et al., 2002, Science 297:1833-1837; Jenuwein, 2002, Science 297:2215-2218; and Hall et al., 2002, Science 297:2232-2237). In another non-limiting example, modulation of gene expression by single-stranded RNA molecules of the invention can result from cleavage of RNA (either coding or non-coding RNA) via RISC, or via translational inhibition, as is known in the art or modulation can result from transcriptional inhibition (see for example Janowski et al., 2005, Nature Chemical Biology 1:216-222).

The terms “inhibit,” “down-regulate,” “reduce” or “knockdown” as used herein refer to their meanings as are generally accepted in the art. With reference to exemplary single-stranded RNAi molecules of the invention, the terms generally refer to the reduction in the (i) expression of a gene or target sequence and/or the level of RNA molecules encoding one or more proteins or protein subunits, and/or (ii) the activity of one or more proteins or protein subunits, below that observed in the absence of the single-stranded RNAi molecules of the invention. Down-regulation can also be associated with post-transcriptional silencing, such as RNAi-mediated cleavage, or by alteration in DNA methylation patterns or DNA chromatin structure. Inhibition, down-regulation, reduction or knockdown with an RNAi agent can be in reference to an inactive molecule, an attenuated molecule, an RNAi agent with a scrambled sequence, or an RNAi agent with mismatches. The phrase “gene silencing” refers to a partial or complete loss-of-function through targeted inhibition of an endogenous target gene in a cell. As such, the term is used interchangeably with RNAi, “knockdown,” “inhibition,” “down-regulation,” or “reduction” of expression of a target gene.

To determine the extent of inhibition, a test sample (e.g., a biological sample from an organism of interest expressing the target gene(s) or target sequence(s) or a sample of cells in culture expressing the target gene/sequence) can be contacted with an RNAi molecule that silences, reduces, or inhibits expression of a target gene or sequence. Expression of the target gene/sequence in the test sample is compared to expression of the target gene/sequence in a control sample (e.g., a biological sample from an organism of interest expressing the target gene/sequence or a sample of cells in culture expressing the target gene/sequence) that is not contacted with the RNAi molecule. Control samples (i.e., samples expressing the target gene/sequence) are assigned a value of 100%. Silencing, inhibition, or reduction of expression of a target gene/sequence is achieved when the value of the test sample relative to the control sample is about 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, or 10%. Suitable assays include, e.g., examination of protein or mRNA levels using techniques known to those of skill in the art, such as dot blots, Northern blots, in situ hybridization, ELISA, microarray hybridization, immunoprecipitation, enzyme function, as well as phenotypic assays known to those of skill in the art.

The phrase “improved RNAi activity” generally refers to an increase in RNAi activity measured in vitro and/or in vivo, where the RNAi activity is a reflection of either or both the ability of the RNAi agent to mediate RNAi and the stability of the RNAi agent.

The term “modulate” as used herein refers to its meaning as is generally accepted in the art. The term generally refers to when the expression of a gene, or level of one or more RNA molecules (coding or non-coding), or activity of one or more RNA molecules or proteins or protein subunits, is up-regulated or down-regulated, such that expression, level, or activity is greater than or less than that observed in the absence of the molecule that effects modulation. For example, the term “modulate” in some embodiments can refer to inhibition and in other embodiments can refer to potentiation or up-regulation, e.g., of gene expression.

The term “RNAi agent” or “RNAi molecule” refers to any nucleic acid molecule capable of inhibiting or down-regulating gene expression or viral replication by mediating RNA interference (“RNAi”) or gene silencing in a sequence-specific manner. The RNAi agent can be a double-stranded nucleic acid molecule comprising self-complementary sense (passenger) and antisense (guide) strands, wherein the antisense strand comprises a nucleotide sequence that is complementary to a nucleotide sequence in a target nucleic acid molecule or a portion thereof, and the sense strand comprises a nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof. An RNAi agent can be a single-stranded polynucleotide. While not wishing to be bound by theory, an RNAi agent may act by one or more of a number of mechanisms, including post-transcriptional cleavage of a target mRNA, or pre-transcriptional or pre-translational mechanisms.

The term “single-stranded RNAi” or “ssRNAi” agent or molecule is an RNAi agent that is a single-stranded, nucleic acid-derived molecule having a nucleotide sequence that is partially, substantially, or perfectly complementary to a nucleotide sequence in a target nucleic acid molecule or a portion thereof. A second nucleotide sequence with which the single-stranded RNAi agent forms base-pairs is not present. A single-stranded RNAi molecule can further comprise a terminal phosphate group located at one or both of the terminal ends, such as a 5′-phosphate or a 5′,3′-diphosphate. An ssRNAi molecule/agent can include a miRNA or a miRNA mimetic. A single-stranded RNAi agent of the invention can be loaded into or otherwise associated with RISC and participate in gene silencing via an RNAi mechanism. A single-stranded RNAi molecule of the invention can comprise substitutions, chemically-modified nucleotides, and non-nucleotides. A single-stranded RNAi molecule of the invention can comprise one or more or all ribonucleotides. Certain embodiments of the invention include single-stranded RNAi molecules that comprise substitutions or modifications in the backbone, sugars, bases, or nucleosides.

The term, “miRNA” or “microRNA” is used herein in accordance with its ordinary meaning in the art and refers to small, non-protein coding RNA molecules that are expressed in a diverse array of eukaryotes, including mammals, and are involved in RNA-based gene regulation. Mature, fully processed miRNAs are about 15 to about 30 nucleotides in length. A representative set of known, endogenous miRNA species is described in the publicly available miRBase sequence database, described in Griffith-Jones et al., Nucleic Acids Research, 2004, 32:D109-D111 and Griffith-Jones et al., Nucleic Acids Research, 2006, 34:D 140-D144, and accessible on the World Wide Web at the Wellcome Trust Sanger Institute website. The mature, fully-processed miRNAs that are publicly available on the miRBase sequence database are each incorporated by reference herein. A representative set of miRNAs is also included herein in Table 1, infra. Each mature miRNA is partially complementary to one or more messenger RNA (mRNA) molecules, which are the targets of the miRNA, thereby regulating the expression of genes associated with the targets.

The term “miRNA mimetic,” as used herein, refers to a single-stranded RNA molecule that is a mimetic of a naturally-occurring miRNA in a cell. A miRNA mimetic is typically designed based on a corresponding, endogenous miRNA. A miRNA mimetic is capable of modulating the expression of a target mRNA that is also regulated by a corresponding, naturally-occurring miRNA. A single-stranded RNAi molecule of the present invention that is also a miRNA mimetic can be loaded into or otherwise associated with RISC and participates in gene silencing via an RNAi mechanism. A miRNA mimetic of the invention can comprise substitutions, chemically-modified nucleotides, and non-nucleotides. A miRNA mimetic of the invention can comprise one or more or all ribonucleotides. Certain embodiments of the invention include miRNA mimetics that comprise substitutions or modifications in the backbone, sugars, bases, or nucleosides. A naturally-occurring miRNA in a cell is referred to herein as “the corresponding miRNA,” “the endogenous miRNA,” or the “naturally-occurring miRNA.” A single-stranded miRNA mimetic of the invention that is provided to a cell is also understood to target one or more target mRNAs that are also targeted by a corresponding, naturally-occurring miRNA. It is contemplated that a miRNA mimetic of the present invention introduced to a cell is capable of functioning as a naturally-occurring miRNA under appropriate conditions.

As used herein, the term “seed region” (also referred to herein as a “seed sequence”) refers to its meaning as is generally accepted in the art. The term generally refers to at least 6 consecutive nucleotides within nucleotide positions 1 to 10 of the 5′-end of a naturally-occurring mature miRNA, such as one selected from those listed in the publicly available miRBase sequence database as of the filing date of the present application and/or one selected from those listed in Table 1. The seed sequence nucleotides of positions 1 to 8 are capitalized in the sequences of Table 1. In a naturally-occurring miRNA, the seed region typically determines the target mRNA sequence to which the miRNA may bind and provide gene regulation. As such, multiple naturally-occurring miRNAs can share a seed region or share substantial homology in the seed regions, and these miRNAs are members of the same miRNA family.

The term “siRNA” (also “short interfering RNA” or “small interfering RNA”) is given its ordinary meaning accepted in the art, generally referring to a duplex (sense and antisense strands) of complementary RNA oligonucleotides which may or may not comprise 3′ overhangs of about 1 to about 4 nucleotides and which mediate RNA interference.

The term “siRNA mimetic” or “single-stranded siRNA mimetic,” as used herein, refers to a single-stranded RNAi molecule that is a mimetic of the guide or antisense strand of a corresponding siRNA (either single or double-stranded). A siRNA mimetic is capable of modulating the expression of a target RNA that is also regulated by the corresponding siRNA and, thus, can be loaded into or otherwise associated with RISC and participates in gene silencing via an RNAi mechanism. A single-stranded siRNA mimetic of the invention can comprise substitutions, chemically-modified nucleotides, and non-nucleotides. A siRNA mimetic of the invention can comprise one or more or all ribonucleotides. Certain embodiments of the invention include siRNA mimetics that comprise substitutions or modifications in the backbone, sugars, bases, or nucleosides.

The term “gene” as used herein, especially in the context of “target gene” for an RNAi agent, refers to the meaning as is generally accepted in the art. The term generally refers to a nucleic acid (e.g., DNA or RNA) sequence that comprises partial length or entire length coding sequences necessary for the production of a polypeptide. The target gene can also include the UTR (i.e., untranslated region) or non-coding region of the nucleic acid sequence. A gene or target gene can also encode a functional RNA (fRNA) or non-coding RNA (ncRNA), such as small temporal RNA (stRNA), micro RNA (miRNA), small nuclear RNA (snRNA), short interfering RNA (siRNA), small nucleolar RNA (snRNA), ribosomal RNA (rRNA), transfer RNA (tRNA) and precursor RNAs thereof. Such non-coding RNAs can serve as target nucleic acid molecules for RNA interference in modulating the activity of fRNA or ncRNA involved in functional or regulatory cellular processes. Aberrant fRNA or ncRNA activity leading to disease can therefore be modulated by the RNAi agents of the invention. RNAi agents targeting fRNA and ncRNA can also be used to manipulate or alter the genotype or phenotype of a subject, organism or cell, by intervening in cellular processes such as genetic imprinting, transcription, translation, or nucleic acid processing (e.g., transamination, methylation etc.). A target gene can be a gene derived from a cell, an endogenous gene, a transgene, or exogenous genes such as genes of a pathogen, for example a virus, which is present in the cell after infection thereof. A cell containing a target gene can be derived from or contained in any organism, for example a plant, animal, protozoan, virus, bacterium, or fungus. Non-limiting examples of plants include monocots, dicots, or gymnosperms. Non-limiting examples of animals include vertebrates or invertebrates. Non-limiting examples of fungi include molds or yeasts. For a review, see for example Snyder and Gerstein, 2003, Science 300:258-260.

The phrases “target site,” “target sequence,” and “target region,” as used herein, refer to their meanings as generally accepted in the art. The terms generally refer to a sequence within a target nucleic acid molecule (e.g., mRNA) that is “targeted,” e.g., for cleavage mediated by an RNAi molecule that contains a sequence within its guide/antisense region that is partially, substantially, or perfectly complementary to that target sequence. A “target site” for a single-stranded RNAi molecule of the present invention refers to a nucleic acid sequence that is partially, substantially, or perfectly complementary to the single-stranded RNAi agent. The target site may be within a coding or a non-coding (i.e., untranslated) region of a target RNA. The target site may be the target site for an endogenous miRNA for which the single-stranded RNAi molecule is a mimetic, in which case the “target site” can also be referred to as a “miRNA target site” or a “corresponding miRNA target site.”

The phrase “sense region” as used herein refers to its meaning as is generally accepted in the art. The term generally refers to a nucleotide sequence of an RNAi molecule having complementarity to an antisense region of the RNAi molecule. In addition, the sense region of an RNAi molecule can comprise a nucleic acid sequence having homology or sequence identity with a target nucleic acid sequence. The sense region of an RNAi molecule is also referred to as the sense strand or the passenger strand.

The phrase “antisense region” as used herein refers to its meaning as is generally accepted in the art. The term generally refers to a nucleotide sequence of an RNAi molecule having complementarity to a target nucleic acid sequence. In addition, the antisense region of an RNAi molecule can optionally comprise a nucleic acid sequence having complementarity to a sense region of the RNAi molecule. The antisense region of an RNAi molecule is also referred to as the antisense strand or the guide strand.

As used herein, the term “spacer” refers to any chemical group(s) capable of linking either two nucleotides and/or non-nucleotide substitute moieties. As used in the present invention, the “spacer” can connect two nucleotides and/or non-nucleotide substitute moieties by traditional phosphodiester bonds or non-phosphodiester connectors. The spacer is typically an organic entity that is covalently bound to each nucleotide or non-nucleotide substitute and is other than the internucleotide linkages that form the backbone (i.e., the nucleobases which form complementary hybrids).

As used herein, the term “alkyl” is intended to include a saturated aliphatic hydrocarbon group, both branched and straight-chain, having a specified number of carbon atoms. The term “alkyl” also refers to non-aromatic cycloalkyl groups. Preferably, an alkyl group has from 1 to 20 carbons (i.e., C₁-C₂₀). For example, C₁-C₁₀, as in “C₁-C₁₀ alkyl” is defined to include groups having 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 carbons in a linear, branched or cyclic arrangement (i.e., cycloalkyl). The term “cycloalkyl” means a monocyclic saturated aliphatic hydrocarbon group having the specified number of carbon atoms. For example, “alkyl” specifically includes methyl, ethyl, n-propyl, i-propyl, n-butyl, t-butyl, i-butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl, and so on, as well as cycloalkyls, including cyclopropyl, methyl-cyclopropyl, 2,2-dimethyl-cyclobutyl, 2-ethyl-cyclopentyl, cyclohexyl, and so on. An alkyl group may be substituted, if indicated.

As used herein, the term “alkenyl” refers to a non-aromatic hydrocarbon radical, straight or branched, containing 2 or more carbon atoms and at least 1 carbon to carbon double bond. The term “alkenyl” also refers to non-aromatic cycloalkenyl groups. Preferably, the alkenyl group has from 1 to 20 carbons (i.e., C₁-C₂₀). Alkenyl groups include, for example, ethenyl, propenyl, butenyl and cyclohexenyl. An alkenyl group may contain double bonds and may be substituted, if indicated.

As used herein, the term “alkynyl” refers to a non-aromatic hydrocarbon radical, straight, or branched, containing 2 or more carbon atoms and at least 1 carbon to carbon triple bond. The term “alkynyl” also refers to non-aromatic cycloalkynyl groups. Up to 3 carbon-carbon triple bonds may be present. Preferably, the alkynyl group has from 1 to 20 carbons (i.e., C₁-C₂₀). Alkynyl groups include, for example, ethynyl, propynyl, butynyl and cyclooctynl. An alkynyl group may contain triple bonds and may be substituted, if indicated.

The term “aliphatic” as used herein in reference to a chemical group refers to an organic group composed of carbon and hydrogen which does not contain aromatic rings. Aliphatic structures can be cyclic and/or saturated. The carbon atoms can be joined together in straight chains, branched chains, or non-aromatic rings. They can also be joined by single bonds (alkanes), double bonds (alkenes) or triple bonds (alkynes). Besides hydrogen, other elements can be bound to the carbon chain or substituted for a carbon within the chain, the most common being oxygen, nitrogen, sulfur and chlorine.

The term “aromatic” as used herein in reference to a chemical group refers to an organic group containing a set of covalently-bound atoms with the following specific characteristics: (1) a delocalized conjugated π system, most commonly an arrangement of alternating single and double bonds; (2) coplanar structure, with all the contributing atoms in the same plane; (3) contributing atoms arranged in one or more rings; and, (4) a number of delocalized it electrons that is even, but not a multiple of 4. An aromatic structure can be composed solely of hydrocarbons (e.g., aryl). Other elements can be bound to or substituted for a carbon of the aromatic structure, the most common being oxygen, nitrogen, sulfur and chlorine (e.g., heteroaryl, substituted aryl, substituted heteroaryl).

The term “substituted” as used in reference to an aliphatic or aromatic organic structure (e.g., an alkyl, alkenyl, alkynyl, aryl) refers to the presence of additional chemical moieties and/or functional groups bound to the carbon chain. For example, a substituted hydrocarbon chain can include a hydrocarbon chain with a heteroatom (e.g., N, O, or S) bound to it. A substituted hydrocarbon chain can also include a hydrocarbon chain that is interrupted with a heteroatom. When substituted, the substituted group(s) is preferably, hydroxyl, halogen, cyano, C1-C4 alkoxy, ═O, ═S, NO₂, SH, NH₂, or NR₁R₂, where R₁ and R₂ independently are H or C₁-C₄ alkyl. A substituted alkyl includes oligomers or polymers of ethylene oxide, including but not limited polyethylene glycol (“PEG”).

The term “non-nucleotide” or “non-nucleic acid” refers to any chemical molecule, moiety, group or compound that is not a nucleotide.

As used herein, the term “substitute non-nucleotide moiety” (or “non-nucleotide substitute moiety”) refers to a chemical moiety that is capable of substituting for one or more nucleotides in a single-stranded RNAi molecule of the invention. Substitute non-nucleotide moieties are typically those that allow for non-traditional base-pairing (i.e., not forming traditional hydrogen bonds). In certain embodiments, substitute non-nucleotide moieties of the instant disclosure are those that are capable of associating or otherwise interacting with one or more components of the cellular RNAi machinery, including, for example, the PAZ domain, the PIWI domain and/or other Argonaute protein domains associated with the RISC.

The term “synthetic,” in certain embodiments herein, refers to nucleic acid molecules that are not produced naturally in a cell. The single-stranded RNAi molecules of the invention are typically synthetic.

In certain embodiments, a single-stranded RNAi molecule of the invention may be isolated. The term “isolated,” as used herein in relation to an oligonucleotide, generally refers to a nucleic acid molecule that exists in a physical form differing from any nucleic acid molecules of identical sequence as found in nature. “Isolated” does not require, although it does not prohibit, that the nucleic acid be physically removed from its native environment. For example, a nucleic acid can be said to be “isolated” when it includes nucleotides and/or internucleoside bonds not found in nature. A nucleic acid can be said to be “isolated” when it exists at a purity not found in nature, where purity can be adjudged with respect to the presence of nucleic acids of other sequences, with respect to the presence of proteins, with respect to the presence of lipids, or with respect to the presence of any other component of a biological cell, or when the nucleic acid lacks sequence that flanks an otherwise identical sequence in an organism's genome, or when the nucleic acid possesses sequence not identically present in nature. A single-stranded RNAi molecule of the present invention can be isolated by virtue of its having been synthesized in vitro. It will be understood, however, that isolated nucleic acids may be subsequently mixed or pooled together.

As used herein, “endogenous” refers its meaning as generally accepted in the art. The term generally refers to any material from or produced inside an organism, cell, tissue or system. As used herein, an “endogenous miRNA” is a naturally-occurring miRNA in a cell, tissue, organism, including a mammal, such as, for example, a human. “Exogenous” generally refers to any material introduced from or produced outside an organism, cell, tissue or system.

The term “expression” as used herein refers to its meaning as is generally accepted in the art. The term generally is defined as the transcription and/or translation of a particular nucleotide sequence driven by its promoter.

In some embodiments, it may be useful to know whether a cell expresses a particular miRNA endogenously or whether such expression is affected under particular conditions or when it is in a particular disease state. Thus in some embodiments of the invention, methods include assaying a cell or a sample containing a cell for the presence of one or more marker genes or mRNA or other analyte indicative of the expression level of a gene of interest. Consequently in some embodiments, methods include a step of generating an RNA profile for a sample. The term “RNA profile” or “gene expression profile” refers to a set of data regarding the expression pattern for one or more gene or genetic marker in the sample (e.g., a plurality of nucleic acid probes that identify one or more markers).

By “capable of” is meant that, when RNAi activity is measured by a suitable in vivo or in vitro assay or method, a single-stranded RNAi molecule of the invention demonstrates at least 5% or more of the knockdown effect against a target sequence as compared to the knockdown effect achieved by the corresponding single-stranded RNAi molecule without the internal, non-nucleotide spacer portion(s). Preferably, a single-stranded RNAi molecule of the invention is capable of achieving 25% or more, 35% or more, 50% or more, 55% or more, 60% or more, 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 99% or more, or even 100% or more (i.e., equal or more potent RNAi activity) knockdown of the target than a corresponding RNAi molecule against the same target (e.g., a naturally-occurring miRNA or previously-identified siRNA guide strand).

A “vector” is a replicon, such as a plasmid, phagemid, cosmid, baculovirus, bacmid, bacterial artificial chromosome (BAC), yeast artificial chromosome (YAC), as well as other bacterial, yeast, or viral vectors, to which another nucleic acid segment may be operatively inserted so as to bring about replication or expression of the inserted segment. “Expression vector” refers to a vector comprising expression control sequences operatively linked to a nucleotide sequence to be expressed. An expression vector comprises sufficient cis-acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system. Expression vectors include all those known in the art, such as cosmids, plasmids (e.g., naked or contained in liposomes), and viruses (e.g., lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses).

The terms “composition” or “formulation” as used herein refer to their generally accepted meaning in the art. These terms generally refer to a composition or formulation, such as in a pharmaceutically acceptable carrier or diluent, in a form suitable for administration, e.g., systemic or local administration, into a cell or subject, including, for example, a human. Suitable forms, in part, depend upon the use or the route of entry, for example oral, transdermal, inhalation, or by injection. Such forms should not prevent the composition or formulation from reaching a target cell (i.e., a cell to which the negatively charged nucleic acid is desirable for delivery). For example, compositions injected into the blood stream should be soluble. Other factors are known in the art, and include considerations such as toxicity and forms that prevent the composition or formulation from exerting its effect. As used herein, pharmaceutical formulations include formulations for human and veterinary use. Non-limiting examples of agents suitable for formulation with the nucleic acid molecules of the instant invention include: Lipid Nanoparticles (see for example Semple et al., 2010, Nat Biotechnol. 28(2):172-6.); P-glycoprotein inhibitors (such as Pluronic P85); biodegradable polymers, such as poly (DL-lactide-coglycolide) microspheres for sustained release delivery (Emerich, D F et al, 1999, Cell Transplant 8:47-58); and loaded nanoparticles, such as those made of polybutylcyanoacrylate. Other non-limiting examples of delivery strategies for the nucleic acid molecules of the instant invention include material described in Boado et al., 1998, J. Pharm. Sci. 87:1308-1315; Tyler et al., 1999, FEBS Lett. 421:280-284; Pardridge et al., 1995, PNAS USA. 92:5592-5596; Boado, 1995, Adv. Drug Delivery Rev., 15:73-107; Aldrian-Herrada et al., 1998, Nucleic Acids Res. 26:4910-4916; and, Tyler et al., 1999, PNAS 96:7053-7058. A “pharmaceutically acceptable composition” or “pharmaceutically acceptable formulation” can refer to a composition or formulation that allows for the effective distribution of the nucleic acid molecules of the instant invention to the physical location most suitable for their desired activity.

The terms “patient,” “subject,” “individual” and the like are used interchangeably herein, and refer to any animal or cells or tissues thereof, whether in vitro or in situ, amendable to the methods described herein. They typically refer to an organism, which is a donor or recipient of the single-stranded RNA molecules of this disclosure. In certain non-limiting embodiments, the patient, subject or individual is a mammal or a mammalian cell. In other non-limiting embodiments, the patient, subject or individual is a human or a human cell.

As used herein, the term “therapeutically effective amount” means an amount of a single-stranded RNAi molecule of the present disclosure that is sufficient to result in a decrease in severity of disease symptoms, an increase in frequency or duration of disease symptom-free periods, or a prevention of impairment or disability due to the disease, in the subject (e.g., a mammal or human) to which it is administered. One of ordinary skill in the art can determine such therapeutically effective amounts based on such factors such as the subject's size, the severity of symptoms, and the particular composition or route of administration selected. For example, a therapeutically effective amount of a single-strand RNAi molecule of the invention, individually, in combination, or in conjunction with other drugs, can be used or administered at a therapeutically effective amount to a subject or by administering to a particular cells under conditions suitable for treatment, to, for example, decrease tumor size, or otherwise ameliorate symptoms associated with a particular disorder in the subject.

The term “therapeutic” as used herein means a treatment and/or prophylaxis. A therapeutic effect is obtained by suppression, remission, or eradication of a disease state. The term “treatment” as used herein is meant to include therapeutic treatment as well as prophylactic, or suppressive measures for diseases or disorders. Thus, for example, the term “treatment” includes the administration of an agent prior to or following the onset of a disease or disorder thereby preventing or removing all signs of the disease or disorder. As another example, administration of the agent after clinical manifestation of the disease to combat the symptoms of the diseases is also comprised by the term “treatment.”

The term “parenteral” as used herein refers to its meaning as is generally accepted in the art. The term generally refers methods or techniques of administering a molecule, drug, agent, or compound in a manner other than through the digestive tract, and includes epicutaneous, subcutaneous, intravascular (e.g., intravenous), intramuscular, or intrathecal injection or infusion techniques and the like.

The phrase “systemic administration” as used herein refers to its meaning as is generally accepted in the art. The term generally refers in vivo systemic absorption or accumulation of drugs in the blood stream followed by distribution throughout the entire body.

Other objects, features and advantages of the present invention will become apparent from the detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating specific embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from the detailed description.

B. Single-Stranded RNAi Molecules of the Invention

The instant disclosure provides single-stranded RNA molecules comprising at least one internal, non-nucleotide spacer that links together two nucleotide portions of the molecule. Thus, a single-stranded RNA molecule of the present invention is not a continuous stretch of nucleotides but comprises more than one nucleotide portion separated by one or more non-nucleotide spacers, wherein the nucleotide portions contain one or more nucleotides, non-nucleotide substitute moieties, or a combination thereof. A single-stranded RNA molecule of the invention functions as a guide or antisense strand that is capable of inhibiting gene expression via an RNA interference mechanism and, thus, represents an RNAi agent. A single-stranded RNAi molecule of the invention comprises sequence that is partially, substantially or perfectly complementary to one or more RNA target sites in a cell.

A single-stranded RNAi molecule of the invention has a single-stranded oligonucleotide structure comprising (a) a nucleic acid portion separated into two or more nucleotide portions, and (b) an internal (as opposed to “terminal”) spacer portion comprising at least one non-nucleotide spacer portion, wherein the non-nucleotide spacer portion(s) covalently links two nucleotides, each within distinct nucleotide portions of the molecule. The nucleotide portions of a single-stranded RNAi molecule of the invention are separated by the non-nucleotide spacer portions, wherein each nucleotide portion contains at least one nucleotide.

In each embodiment of the invention, the nucleic acid portion of a single-stranded RNAi molecule contains at least two nucleotide portions, a first nucleotide portion (N1) (e.g., a 5′-nucleotide portion) and a second nucleotide portion (N2) (e.g., a 3′-nucleotide portion). The nucleic acid portion of a single-stranded RNAi molecule of the invention can comprise more than two nucleotide portions (e.g., a third nucleotide portion (N3), a fourth nucleotide portion (N4) etc.). Within each nucleotide portion of an RNAi molecule of the invention, the nucleotides and/or non-nucleotide moieties are connected by phosphodiester bonds and/or non-phosphodiester connectors. Importantly, the nucleotide portions of a single-stranded RNAi molecule of the invention are not complementary to each other and, thus, said portions do not form significant base-pairing.

In each embodiment of the invention, the internal spacer portion of a single-stranded RNAi molecule contains at least one non-nucleotide spacer portion (S1), referred to here in as a first non-nucleotide spacer portion. In one embodiment of the present invention, a single-stranded RNAi molecule contains one internal, non-nucleotide spacer portion. The internal spacer portion of a single-stranded RNAi molecule of the invention can comprise more than a first non-nucleotide spacer portion (e.g., a second non-nucleotide spacer portion (S2), a third non-nucleotide spacer portion (S3) etc.). In another embodiment, a single-stranded RNAi molecule contains two internal, non-nucleotide spacer portions.

The number of nucleotide portions within the nucleic acid portion of a single-stranded RNAi molecule of the present invention is dependent on the number of non-nucleotide spacer portions within the molecule, and vice versa. For example, if a single-stranded RNAi molecule contains two non-nucleotide spacer portions, it will generally contain three nucleotide portions, as follows: 5′-(first nucleotide portion)-(first non-nucleotide spacer portion)-(second nucleotide portion)-(second non-nucleotide spacer portion)-(third nucleotide portion)-3′. Each non-nucleotide spacer portion of a single-stranded RNAi molecule of the present invention can contain one or more non-nucleotide spacers.

Single-stranded RNAi molecules of the invention have a single-stranded oligonucleotide structure and mediate RNA interference against a target RNA. Single-stranded RNAi molecule of the invention can comprise: (a) a nucleic acid portion comprising a first nucleotide portion (N1) and a second nucleotide portion (N2), wherein said nucleic acid portion comprises at least 8 nucleotides that can base pair with a target site within a target RNA, and wherein the total number of nucleotides within the nucleic acid portion is from 8 to 26 nucleotides; and, (b) an internal spacer portion comprising at least a first non-nucleotide spacer portion (S1) that covalently links the first and second nucleotide portions. The first and second nucleotide portions are not self complementary. All of nucleotides (e.g., 8 to 26) of a single-stranded RNAi molecule of the invention, all located within the nucleic acid portion, are distributed between the nucleotide portions of the molecule, wherein each nucleotide portion contains at least one nucleotide.

In one embodiment, a single-stranded RNAi molecule of the invention comprises a nucleic acid portion containing a total of from 8 to 26 nucleotides or non-nucleotide substitute moieties (e.g., 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides or non-nucleotide substitute moieties) distributed between the nucleotide portions of the oligonucleotide, wherein at least 8 (e.g., 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26) of the nucleotides in the molecule can base pair with a target site within a target RNA. For example, a single-stranded RNAi molecule of the invention may contain 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 total nucleotides, wherein 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 of those nucleotides base pair with a target RNA. In one embodiment, the nucleic acid portion of a single-stranded RNAi molecule of the invention contains a total of from 15 to 21 (e.g., 15, 16, 17, 18, 19, 20, or 21) nucleotides. In another embodiment, the nucleic acid portion of a single-stranded RNAi molecule of the invention contains a total of from 18 to 20 (e.g., 18, 19, or 20) nucleotides. In a further embodiment, the nucleic acid portion of a single-stranded RNAi molecule of the invention contains a total of 19 or 20 nucleotides.

The total number of nucleotides or non-nucleotide moieties, or a combination thereof, that make up the nucleotide portions of a single-stranded RNAi molecule of the invention is distributed between those portions of the molecule in any number of ways. As an example, a single-stranded RNAi molecule comprising only one non-nucleotide spacer portion and two nucleotide portions (i.e., the first nucleotide portion and the second nucleotide portion) may have a total of 12 nucleotides. If the first nucleotide portion of the molecule contains a single nucleotide (e.g., at the 5′-terminus of the molecule), the second nucleotide portion of the molecule will contain 11 contiguous nucleotides. Alternatively, if the first nucleotide portion of the molecule contains 5 contiguous nucleotides, the second nucleotide portion of the molecule will contain 7 contiguous nucleotides. In each example, the total number of nucleotides in the molecule is 12. The nucleotides within the nucleotide portions of a single-stranded RNAi molecule of the invention are not complementary to each other and, thus, said portions can not form substantial base-pairing. Within each of the nucleotide portions of the molecule, the nucleotides and/or non-nucleotide moieties are connected by phosphodiester bonds and/or non-phosphodiester connectors.

At least 8 nucleotides within the nucleic acid portion of a single-stranded RNAi molecule of the invention can base pair with a target sequence within a target RNA. Thus, the single-stranded RNAi molecules of the invention comprise a sequence of contiguous nucleotides that is partially, substantially or perfectly complementary to an RNA target site, including a naturally-occurring RNA target site. In one embodiment, all of the contiguous nucleotides within the nucleic acid portion of a single-stranded RNAi molecule of the invention base pair with a target sequence within a target RNA (i.e., perfectly complementary). In another embodiment, at least 50% of the contiguous nucleotides within the nucleic acid portion of a single-stranded RNAi molecule of the invention base pair with a target sequence within a target RNA (i.e., substantially complementary). In another embodiment, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides within the nucleic acid portion of a single-stranded RNAi molecule of the invention base pair with a target sequence within a target RNA.

In one embodiment, a single-stranded RNAi molecule of the invention has a single-stranded oligonucleotide structure comprising: (a) two nucleotide portions, a first nucleotide portion (N1) and a second nucleotide portion (N2); and, (b) one internal, non-nucleotide spacer portion (S1); wherein the oligonucleotide contains a total of from 8 to 26 nucleotides or non-nucleotide substitute moieties (e.g., 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides or non-nucleotide substitute moieties); and wherein at least 8 of the nucleotides of the molecule can base pair with a target site within a target RNA. The two nucleotide portions of a single-stranded RNAi molecule of this embodiment comprise, in sum, 8 to 26 (e.g., 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or, 26) nucleotides or non-nucleotide moieties, or a combination thereof, that are distributed between the two nucleotide portions in any number of ways (as described above). In one embodiment, the non-nucleotide spacer portion contains one non-nucleotide spacer. In another embodiment, the non-nucleotide spacer portion contains more than one non-nucleotide spacer (e.g., 2, 3, 4, or more). The spacer portion links the first and second nucleotide portions of the single-stranded RNAi molecule. Thus, the spacer portion is covalently linked to both the 3′-terminal nucleotide or non-nucleotide substitute moiety of the first nucleotide portion of the molecule and the 5′-terminal nucleotide or non-nucleotide substitute moiety of the second nucleotide portion of the molecule. The spacer portion of the molecule can be covalently connected to the phosphate backbone of the nucleotide portions (i.e., through the free phosphate of the two, linked nucleotides) by either traditional phosphodiester bonds or non-phosphodiester connectors.

In one embodiment, a single-stranded RNAi molecule of the invention comprises a contiguous nucleotide sequence that is partially, substantially or perfectly homologous to the guide strand of a naturally-occurring miRNA and, thus, functions as a miRNA mimetic. In another embodiment, a single-stranded RNAi molecule of the invention comprises a contiguous nucleotide sequence that is partially, substantially or perfectly homologous to either a single-stranded siRNA or the guide/antisense strand of a duplex siRNA and, thus, functions as a siRNA mimetic. The single-stranded siRNA or duplex siRNA may be known to inhibit gene expression via an RNAi mechanism.

If a single-stranded RNAi molecule of the present invention is an analog of a naturally-occurring miRNA, the naturally-occurring miRNA is referred to herein as “the corresponding miRNA,” and the single-stranded RNAi molecule represents a mimetic of the corresponding miRNA. A single-stranded miRNA mimetic of the present invention is designed based on a corresponding, naturally-occurring miRNA, wherein at least one non-nucleotide spacer portion is either inserted between two nucleotides of the miRNA guide strand sequence or substituted for one or more nucleotides of the miRNA guide strand sequence. A single-stranded miRNA mimetic of the present invention can be an analog of a mature miRNA sequence publicly available in the miRBase database and/or included within Table 1, infra (SEQ ID NOs: 1-1090).

In one embodiment, a single-stranded RNAi molecule as described herein represents a miRNA mimetic, wherein the RNAi molecule comprises a nucleic acid portion of two or more nucleotide portions and an internal spacer portion comprising at least one non-nucleotide spacer portion. As described above, if the nucleic acid portion of the molecule contains only two nucleotide portions (i.e., a first nucleotide portion and a second nucleotide portion), only one non-nucleotide spacer portion will be present. If the nucleic acid portion of the molecule contains three nucleotide portions, two non-nucleotide spacer portions will be present. Each non-nucleotide spacer portion can comprise more than one non-nucleotide spacer (e.g., 2, 3, 4 or more). In one embodiment, the nucleic acid portion of an miRNA mimetic of the invention consists of from 8 to 26 (e.g., 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26) nucleotides or non-nucleotide moieties, or a combination thereof, wherein at least 8 of the nucleotides can base pair with a naturally-occurring miRNA target site. A contiguous nucleotide sequence within the nucleic acid portion of an miRNA mimetic of the invention is partially, substantially or perfectly homologous to a naturally-occurring miRNA guide strand nucleotide sequence. In one embodiment, a contiguous nucleotide sequence within a nucleic acid portion of a single-stranded RNAi molecule of the invention comprises 5 to 8 (i.e., 5, 6, 7, or 8) contiguous nucleotides that are identical (or perfectly homologous) to the whole or a part of a seed sequence of a naturally-occurring miRNA. For example, in one embodiment, an 8 consecutive nucleotide sequence within a nucleotide portion of a single-stranded RNAi molecule is identical to all or a portion of the seed region of a naturally-occurring miRNA (see Table I, infra).

In one embodiment, a miRNA mimetic of the invention has a non-nucleotide spacer portion and two nucleotide portions, wherein the non-nucleotide spacer portion is inserted between two nucleotides of a corresponding, naturally-occurring miRNA sequence, separating the full-length, naturally-occurring miRNA into two distinct nucleotide portions. In another embodiment, more than one non-nucleotide spacer portion is present in a miRNA mimetic of the invention such that the nucleic acid portion of the miRNA mimetic is separated into more than two nucleotide portions. In such cases, the total nucleotide sequence of the miRNA mimetic is perfectly homologous to the corresponding, naturally-occurring miRNA nucleotide sequence. The difference between the naturally-occurring miRNA and the miRNA mimetic in this embodiment is the presence of a non-nucleotide spacer portion.

In another embodiment, a miRNA mimetic of the invention comprises a non-nucleotide spacer portion that substitutes for one or more nucleotides of a naturally-occurring miRNA guide strand sequence. For example, one or more nucleotides may be first deleted from a naturally-occurring miRNA guide strand sequence, leaving a gap in the sequence and producing at least two distinct nucleotide portions. A non-nucleotide spacer portion is then inserted into the gap, covalently linking the distinct nucleotide portions. Thus, in one embodiment, a single-stranded RNAi molecule of the invention represents a miRNA mimetic wherein one or more internal, non-nucleotide spacer portions takes the place of from one to 12 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12) nucleotides of a corresponding, naturally-occurring miRNA sequence (see SEQ ID NOs: 1-1090). A miRNA mimetic may contain more than one non-nucleotide spacer portion. In one embodiment, a single-stranded miRNA mimetic of the invention comprises at least one non-nucleotide spacer portion in the place of from one to 4 (e.g., 1, 2, 3, or 4) nucleotides of a naturally-occurring miRNA nucleotide sequence. In another embodiment, a single-stranded miRNA mimetic of the invention comprises at least one internal, non-nucleotide spacer portion in the place of one or two nucleotides of a corresponding miRNA nucleotide sequence. The non-nucleotide spacer portion bridges the gap resulting from removal of the one or more nucleotides from a miRNA guide strand sequence, connecting by either traditional phosphodiester bonds or non-phosphodiester connectors to the phosphate backbone of the nucleotide portions of the molecule.

Single-stranded RNAi molecules of the invention can also represent an analog of the guide or antisense strand of a duplex or single-stranded siRNA. The duplex or single-stranded siRNA may be known to inhibit target gene expression, or have the potential of inhibiting target gene expression, via an RNAi mechanism. In such a scenario, the siRNA counterpart, and specifically the guide strand of the siRNA (whether single- or double-stranded), is referred to herein as “the corresponding siRNA” or “the corresponding siRNA guide strand,” and the single-stranded RNAi molecule represents a mimetic of the corresponding siRNA guide strand (i.e., “a single-stranded siRNA mimetic”). A single-stranded siRNA mimetic is designed based on the nucleotide sequence of a corresponding siRNA by either inserting one or more internal, non-nucleotide spacer portions within the nucleotide sequence of the corresponding siRNA nucleotide sequence or substituting one or more nucleotides of the corresponding siRNA nucleotide sequence with one or more non-nucleotide spacer portions.

In one embodiment, a single-stranded RNAi molecule of the invention represents a siRNA mimetic, wherein the nucleic acid portion of the single-stranded RNAi molecule comprises two or more nucleotide portions, and the internal spacer portion comprises at least one non-nucleotide spacer portion. As described above, if the nucleic acid portion of the RNAi molecule contains only two nucleotide portions (i.e., a first nucleotide portion and a second nucleotide portion), only one non-nucleotide spacer portion will be present. If the nucleic acid portion of the RNAi molecule contains three nucleotide portions, two non-nucleotide spacer portions will be present. A non-nucleotide spacer portion may comprise more than one non-nucleotide spacer (e.g., 2, 3, 4 or more). In one embodiment, the nucleic acid portion of a siRNA mimetic consists of from 8 to 26 (e.g., 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26) nucleotides or non-nucleotide moieties, or a combination thereof, wherein at least 8 of the nucleotides can base pair with the an RNA target site. The nucleic acid portion of a siRNA mimetic of the invention comprises a contiguous nucleotide sequence that is partially, substantially or perfectly homologous to a corresponding siRNA guide strand nucleotide sequence.

In one embodiment, a siRNA mimetic of the invention has a non-nucleotide spacer portion and two nucleotide portions, wherein the non-nucleotide spacer portion is inserted between two adjacent nucleotides of the corresponding siRNA nucleotide sequence, separating the corresponding siRNA nucleotide sequence into two distinct nucleotide portions. In another embodiment, a siRNA mimetic of the invention can have more than one non-nucleotide spacer portion such that the corresponding siRNA nucleotide sequence is separated into more than two nucleotide portions. In such cases, the total nucleotide sequence of the siRNA mimetic is perfectly homologous to the corresponding siRNA nucleotide sequence. The difference between the corresponding siRNA and the siRNA mimetic in this embodiment is the presence of a non-nucleotide spacer region(s).

In another embodiment, a siRNA mimetic of the invention comprises one or more non-nucleotide spacer portions that substitutes for one or more nucleotides of a corresponding siRNA guide strand nucleotide sequence. For example, one or more nucleotides may be first deleted from a corresponding siRNA nucleotide sequence, leaving a gap in the sequence and producing at least two distinct nucleotide portions. A non-nucleotide spacer portion is then inserted into the gap to link the distinct nucleotide portions. Thus, in one embodiment, a single-stranded RNAi molecule of the present invention represents a siRNA mimetic comprising at least one internal, non-nucleotide spacer portion, wherein said non-nucleotide spacer portion takes the place of from one to 4 (e.g., 1, 2, 3, or 4) nucleotides of a corresponding siRNA nucleotide sequence. The siRNA mimetic may contain more than one non-nucleotide spacer portion. In another embodiment, a single-stranded RNAi molecule of the present invention represents a siRNA mimetic comprising at least one internal, non-nucleotide spacer portion, wherein said non-nucleotide spacer portion takes the place of one or two nucleotides of a corresponding siRNA nucleotide sequence. The non-nucleotide spacer portion(s) bridges the gap resulting from removal of the one or more nucleotides from the siRNA guide strand sequence, connecting by either traditional phosphodiester bonds or non-phosphodiester connectors to the phosphate backbone of the nucleotide portions of the molecule.

In another embodiment, single-stranded RNAi molecules of the invention can be designed de novo for the purpose of knocking down expression of a particular RNA target, including a naturally-occurring RNA target. In this scenario, a target gene is first selected. One of skill in the art then identifies a portion of said gene (i.e., the target site), generally between about 8 and about 26 nucleotides in length, to target with a single-stranded RNAi molecule for gene silencing. In one embodiment of the invention, a contiguous nucleotide sequence within the nucleic acid portion of a single-stranded RNAi molecule described herein is partially, substantially or perfectly complementary to the identified target site sequence and partially, substantially or perfectly homologous to the complement of the corresponding target site sequence. The counterpart sequence of the single-stranded RNAi molecule in this scenario (i.e., a nucleotide sequence that is the complement of the target site sequence) is referred to herein as “the complement of the corresponding target site sequence.” The single-stranded RNAi molecule comprises two or more nucleotide portions and at least one internal, non-nucleotide spacer portion, as described in one or more of the embodiments above.

A single-stranded RNAi molecule of the present invention is capable of producing an RNA interference result. In the case of a single-stranded miRNA mimetic of the invention, the molecule is capable of modulating the expression of a target mRNA that is also regulated by a corresponding naturally-occurring miRNA.

The single-stranded RNAi molecules of the disclosure can further comprise a terminal phosphate group located at one or both of the terminal ends, such as a 5′-phosphate or a 5′,3′-diphosphate. In some embodiments, a single-stranded RNAi molecule of the invention can comprise substitutions, chemically-modified nucleotides, and non-nucleotides. In certain other embodiments, a single-stranded RNAi molecule of the invention can comprise one or more or all ribonucleotides. Certain embodiments of the invention include single-stranded RNAi molecules that comprise substitutions or modifications in the backbone, sugars, bases, or nucleosides.

The internal, non-nucleotide spacer portion(s) of the single-stranded RNAi molecules of the disclosure, especially in situations where the total number of nucleotides in the resulting RNAi molecule is reduced compared to a corresponding RNAi agent of which the single-stranded RNAi molecule is an analog (e.g., a naturally-occurring miRNA; the guide strand of a siRNA with gene knockdown capability), reduces the susceptibility of the single-stranded RNAi molecule to endonucleases. The internal, non-nucleotide spacer portion(s) can also limit the damage of exonucleases, ultimately helping to preserve the integrity of the single-stranded RNAi agent. The spacer portion also represents an easily accessible region for connecting one or more moieties of interest to the RNAi molecule (e.g., a chemical moiety that facilitates cellular delivery). Therefore, even if the activity of a single-stranded RNAi molecule of this disclosure is somewhat reduced (e.g., by less than about 20%, or 30%, or even 40%) as compared to a corresponding single-stranded RNAi molecule without the spacer portion (e.g., a naturally-occurring miRNA; the guide strand of a previously identified siRNA with gene knockdown capability), the overall activity of the analog can be greater than that of its counterpart due to improved stability or delivery of the molecule. Additionally, since the yield of synthesis is usually higher for shorter RNA strands, the cost of large-scale synthesis in connection with therapeutic applications may also be substantially reduced using the single-stranded RNAi molecules of the present invention.

In one embodiment, a single-stranded RNAi molecule of the invention can be represented or depicted by Formula III: 5′ N1-S1-N2 3′ wherein N1, representing a first nucleotide portion, consists of either one nucleotide or a contiguous stretch of nucleotides; S1, representing a non-nucleotide spacer portion, consists of one or more non-nucleotide spacers; and N2, representing a second nucleotide portion, consists of either one nucleotide or a contiguous stretch of nucleotides. The total number of nucleotides in N1 and N2 is from 8 to 26 (e.g., 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26) nucleotides, and at least 8 nucleotides of the molecule can base pair with a target site within a target RNA. The “nucleotide(s)” within N1 and N2 are either nucleotides, modified nucleotides, nucleotide analogs, or non-nucleotides substitute moieties, or a combination thereof. In one embodiment, individually, N1 and N2 can consist of between one and 25 nucleotides, wherein the sum of N1 and N2 is from 8 to 26 (e.g., 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26) nucleotides. N1 and N2 are not self complementary and, thus, cannot participate in substantial base-pairing with each other. Within a contiguous stretches of nucleotides of the molecule, the nucleotides are connected by phosphodiester bonds and/or non-phosphodiester connectors. The spacer portion (S1) is covalently attached to the 3′-terminal nucleotide of the first nucleotide portion (N1) and the 5′-terminal nucleotide of the second nucleotide portion of the molecule (N2). For example, the spacer portion can comprise one or more phosphoramidite spacers attached to the free phosphate group of the adjacent nucleotides by a phosphodiester bond. The spacer portion of the molecule (S1) can consist of a single non-nucleotide spacer or more than one non-nucleotide spacers linked together. If there is more than one non-nucleotide spacer within the S1 portion of the molecule, the spacers can be either the same (i.e., having the same structure) or different (i.e., having different structures). In the case where two non-nucleotide spacers are linked within the S1 portion of the molecule, each spacer is covalently attached to one nucleotide within the N1 and N2 portions of the molecule, respectively. If three non-nucleotide spacers are consecutively linked within the S1 portion of the oligonucleotide, the internal (second) spacer does not form a covalent bond with either the N1 or N2 portions of the molecule. Instead, the internal spacer is covalently attached to the first and third spacers, linking them together.

In another embodiment, a single-stranded RNAi molecule of the invention can be represented or depicted by Formula IV: 5′ N1-S1-N2-S2-N3 3′ wherein N1, representing a first nucleotide portion, consists of either one nucleotide or a contiguous stretch of nucleotides; S1, representing a first non-nucleotide spacer portion, consists of one or more non-nucleotide spacers; N2, representing a second nucleotide portion, consists of either one nucleotide or a contiguous stretch of nucleotides; S2, representing a second non-nucleotide internal spacer portion, consists of one or more non-nucleotide spacers; and, N3, representing a third nucleotide portion, consists of either one nucleotide or a contiguous stretch of nucleotides. In one embodiment, the total number of nucleotides in N1, N2, and N3 is from 8 to about 26 (e.g., 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26) nucleotides, and at least 8 nucleotides of the molecule can base pair with a target site within a target RNA. The “nucleotide(s)” within N1, N2 and N3 are either nucleotides, modified nucleotides, nucleotide analogs, or non-nucleotides substitute moieties, or a combination thereof. In one embodiment, individually, the nucleotide portions (N1, N2, N3) can consist of between one and 24 nucleotides, wherein the sum of nucleotides within the molecule is from 8 to 26 nucleotides. The nucleotide portions of the RNAi molecule are not self complementary and, thus, cannot participate in substantial base-pairing with each other. Within each of the contiguous stretches of nucleotides, the nucleotides are connected by phosphodiester bonds and/or non-phosphodiester connectors. The spacer portions are covalently attached to terminal nucleotides of the nucleotide portions of the molecule. In one embodiment, a spacer portion comprises one or more phosphoramidite spacers attached to the free phosphate groups of adjacent nucleotides by phosphodiester bonds. Each spacer portion of the molecule can consist of a single non-nucleotide spacer or more than one non-nucleotide spacer linked together. If there is more than one non-nucleotide spacer within a spacer portion of the molecule, the spacers can be either the same (i.e., having the same structure) or different (i.e., having different structures). When two non-nucleotide spacers are linked within a spacer portion of the molecule, each spacer is covalently attached to a terminal nucleotide within the adjacent nucleotide portions of the molecule. If three non-nucleotide spacers are consecutively linked within a spacer portion of the molecule, the internal (second) spacer does not form a covalent bond with a nucleotide portion of the molecule. Instead, the internal spacer is covalently attached to the first and third spacers, linking them together.

In one aspect of the invention, at least one nucleotide portion of a single-stranded RNAi molecule described herein (e.g., N1, N2, or N3, as described in Formulas III and/or IV) is a contiguous stretch of nucleotides that consists of either from 1 to 20 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) nucleotides, from 5 to 20 (e.g., 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) nucleotides, from 10 to 20 (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) nucleotides, from 13 to 20 (e.g., 13, 14, 15, 16, 17, 18, 19, or 20) nucleotides, from 5 to 15 (e.g., 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15) nucleotides, or from 1 to 14 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14) nucleotides. In another aspect, the length of at least one nucleotide portion of a single-stranded RNAi molecule of the invention is selected from the group consisting of 18 contiguous nucleotides, 19 contiguous nucleotides, or 20 contiguous nucleotides. In a still further aspect, the length of at least one nucleotide portion of a single-stranded RNAi molecule of the invention is selected from the group consisting of 13 contiguous nucleotides, 14 contiguous nucleotides, or 15 contiguous nucleotides. The length of at least one nucleotide portion of a single-stranded RNAi molecule of the invention can be 18 nucleotides. The length of at least one nucleotide portion of a single-stranded RNAi molecule of the invention can be 19 nucleotides. The length of at least one nucleotide portion of a single-stranded RNAi molecule of the invention can be 20 nucleotides. The length of at least one nucleotide portion of a single-stranded RNAi molecule of the invention can be 21 nucleotides.

In one embodiment, a single-stranded RNAi molecule of the invention is represented by Formula III, wherein N1 consists of 18 contiguous nucleotides; S1 consists of a non-nucleotide spacer; and N2 consists of two contiguous nucleotides. In another embodiment, a single-stranded RNAi molecule of the invention is represented by Formula III, wherein N1 consists of 19 contiguous nucleotides; S1 consists of a non-nucleotide spacer; and N2 consists of one nucleotide. In these embodiments, S1 can be a C3- or C6-alkyl spacer.

In another aspect of the invention, a nucleotide portion of a single-stranded RNAi molecule (e.g., N1, N2, or N3, as described by Formulas III and/or IV) is a contiguous stretch of nucleotides that comprises a sequence of at least 10 (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 etc.) nucleotides that is substantially or perfectly complementary to an RNA target region. In another aspect, a nucleotide portion of a single-stranded RNAi molecule comprises a sequence of from 5 to 8 contiguous nucleotides that is substantially or perfectly complementary to a RNA target region. In this portion of the invention, said nucleotide portion of the molecule is a contiguous stretch of nucleotides that consists of either from 1 to 20 nucleotides, from 5 to 20 nucleotides, from 10 to 20 nucleotides, from 13 to 20 nucleotides, from 5 to 15 nucleotides, or from 1 to 14 nucleotides. In another aspect, said nucleotide portion is 18, 19, or 20 contiguous nucleotides in length. In a still further aspect, said nucleotide portion is 13, 14 or 15 contiguous nucleotides in length. In another aspect, the length of said nucleotide portion is selected from the group consisting of 18 contiguous nucleotides, 19 contiguous nucleotides, or 20 contiguous nucleotides. In a still further aspect, the length of said nucleotide portion is selected from the group consisting of 13 contiguous nucleotides, 14 contiguous nucleotides, or 15 contiguous nucleotides. The length of said nucleotide portion can be 18 nucleotides. The length of said nucleotide portion can be 19 nucleotides. The length of said nucleotide portion can be 20 nucleotides. The length of said nucleotide portion can be 21 nucleotides.

In one embodiment, a nucleotide portion of a single-stranded RNAi molecule of the invention comprises from 5 to 8 (e.g., 5, 6, 7, or 8) contiguous nucleotides that are identical (or perfectly homologous) to the whole or a part of a seed sequence of a naturally-occurring miRNA sequence. In one embodiment, the naturally-occurring miRNA sequence is a sequence recited in Table 1, infra. For example, in one embodiment, a 6-nucleotide sequence within a nucleotide portion of a single-stranded RNAi molecule is identical to all or a portion of the seed region of a naturally-occurring miRNA sequence, including a naturally-occurring miRNA sequence selected from Table 1.

In one embodiment, a single-stranded RNAi molecule of the invention can be represented or depicted by Formula III or Formula IV. It should be appreciated that Formulas III and IV represent particular examples of single-stranded RNAi molecules of the present invention. Additional examples encompassed by the present invention include, but are not limited to, RNAi molecules having more than three nucleotide portions.

In one aspect of the present invention, a contiguous nucleotide sequence within the nucleic acid portion of a single-stranded RNAi molecule is partially, substantially, or perfectly homologous to a naturally-occurring endogenous miRNA or to a guide strand of a siRNA. In another aspect of the invention, a contiguous nucleotide sequence within the nucleic acid portion of a single-stranded RNAi molecule is partially, substantially, or perfectly complementary to a target site within a RNA target sequence. In another embodiment, at least one nucleotide portion of a single-strand RNAi molecule of the disclosure is partially, substantially or perfectly homologous to a region of a naturally-occurring endogenous miRNA or the guide strand of a siRNA and/or partially, substantially or perfectly complementary to a target site within a RNA target sequence.

The internal spacer portion of single-stranded RNAi molecules of the invention comprises at least a first non-nucleotide spacer portion. Said non-nucleotide spacer portion comprises a chemical group, typically an organic entity, covalently bound to, and thus linking, at least two nucleotides. The two nucleotides are within distinct nucleotide portions of the molecule. There is no particular limitation in the length of a non-nucleotide spacer portion as long as it does not severely impact the ability of the molecule to form traditional or non-traditional Watson-Crick base pairing with an RNA target sequence and/or to mediate RNAi. A non-nucleotide spacer portion can connect two nucleotides and/or non-nucleotide substitute moieties by traditional phosphodiester bonds or non-phosphodiester connectors. Single-stranded RNAi molecules of the invention comprising non-phosphodiester based connectors linking the nucleotides and/or non-nucleotides to a spacer include, for example, a peptide-based connector, such as one linking the units of an oligo peptide nucleic acid (PNA) (see Boffa et al., 2000, Gene Ther. Mol. Biol. 5:47-53).

Various non-nucleotide moieties as are provided herein or otherwise known in the art can be included within the internal spacer portion of the single-stranded RNAi molecules of the invention. The non-nucleotide spacers comprised within the internal spacer portion of a single-stranded RNAi molecule of the invention can include any non-nucleic acid spacer capable of linking either two nucleotides and/or non-nucleotide substitute moieties by either traditional phosphodiester bonds or non-phosphodiester connectors. The spacer is typically an aliphatic or aromatic organic entity and is other than the internucleotide linkages that form the backbone of the oligonucleotide (i.e., the nucleobases which form complementary hybrids).

Non-limiting examples of non-nucleotide spacers include the following: a polyether, polyamine, polyamide, peptide, carbohydrate, lipid, polyhydrocarbon, or other polymeric compounds (e.g., polyethylene glycols such as those having between 2 and 100 ethylene glycol units). Specific examples include those described by Seela and Kaiser, 1990, Nucleic Acids Res. 18:6353; Seela and Kaiser, 1987, Nucleic Acids Res. 15:3113; Cload and Schepartz, 1991, J. Am. Chem. Soc. 113:6324; Richardson and Schepartz, 1991, J. Am. Chem. Soc. 113:5109; Ma et al., 1993, Nucleic Acids Res. 27:2585; Ma et al., 1993, Biochemistry 32:1751; Durand et al., 1990, Nucleic Acids Res. 18:6353; McCurdy et al., 1991, Nucleosides & Nucleotides 70:287; Jaschke et al., 1993, Tetrahedron Lett. 34:301; Ono et al., 1991, Biochemistry 30:9914; and others.

In one embodiment of the invention, a spacer is an alkyl, alkenyl or alkynyl chain of from one to 20 carbons (i.e., C1 to C20), preferably from 1 to 12 carbons (i.e., C1 to C12), that is optionally substituted. The hydrocarbon chains can be substituted with additional chemical and/or functional groups (e.g., a moiety that binds specifically to a target molecule of interest).

A chemical moiety that provides additional functionality (e.g., specifically binds to a target molecule of interest or facilitates/enhances cellular delivery of the molecule) to a single-stranded RNAi molecule may be a part of the spacer or covalently attached or linked thereto (e.g., substituted). For example, an additional functional group can impart therapeutic activity to a single-stranded RNAi molecule by assisting in transferring the RNAi molecule compounds across cellular membranes, altering the pharmacokinetics, and/or modulating the localization of RNAi molecules of the invention.

Examples of specific conjugate molecules that may be incorporated within a non-nucleotide spacer itself and/or covalently attached thereto and are contemplated by the instant disclosure are small molecules, lipids or lipophiles, terpenes, phospholipids, antibodies, toxins, cholesterol, a protein binding agent (e.g., a ligand for a cellular receptor that can facilitate cellular uptake), a vitamin, negatively charged polymers and other polymers, for example proteins (e.g., human serum albumin), peptides, hormones, carbohydrates, polyethylene glycols, or polyamines, and those described in, for example, U.S. Patent Publication No. 2005/0196781, and U.S. Patent Publication No. 2006/0293271, the disclosures of which are incorporated herein by reference. These compounds are expected to improve delivery and/or localization of single-stranded RNAi molecules of the invention into a number of cell types originating from different tissues, in the presence or absence of serum (see Sullenger and Cech, U.S. Pat. No. 5,854,038). For example, a conjugate member can be naproxen, nitroindole (or another conjugate that contributes to stacking interactions), folate, ibuprofen, or a C5 pyrimidine linker. In other embodiments, a conjugate member is a glyceride lipid conjugate (e.g., a dialkyl glyceride derivatives), vitamin E conjugates, or thio-cholesterols. In another embodiment, a conjugate molecule is a peptide that functions, when conjugated to a single-stranded RNAi molecule, to facilitate delivery of the molecule into a target cell, or otherwise enhance delivery, stability, or activity of the molecule when contacted with a biological sample. Exemplary peptide conjugate members for use within these aspects of this disclosure, include peptides PN27, PN28, PN29, PN58, PN61, PN73, PN158, PN159, PN173, PN182, PN202, PN204, PN250, PN361, PN365, PN404, PN453, and PN509 as described, for example, in U.S. Patent Application Publication Nos. 2006/0040882 and 2006/0014289, and U.S. Provisional Patent Application No. 60/939,578, which are all incorporated herein by reference.

In one embodiment, a non-nucleotide spacer comprises a moiety that specifically binds to a target molecule. The target molecule can be any molecule of interest. For example, the target molecule can be a ligand-binding domain of a protein, thereby preventing or competing with the interaction of the naturally-occurring ligand with the protein. This is a non-limiting example and those in the art will recognize that other embodiments can be readily generated using techniques generally known in the art (see, e.g., Gold et al, 1995, Annu. Rev. Biochem. 64:163; Brody and Gold, 2000, J. Biotechnol. 74:5; Sun, 2000, Curr. Opin. Mol. Ther. 2:100; Kusser, J., 2000, Biotechnol. 74:21; Hermann and Patel, 2000, Science 257:820; and Jayasena, 1999, Clinical Chem. 45:1628). The spacer portion of a single-stranded RNAi molecule of this disclosure can also conveniently be used to introduce functional chemical groups to an RNAi molecule to enhance properties associated with cellular delivery.

In one embodiment, a conjugate molecule or functional chemical moiety attached via a spacer region of a single-stranded RNAi molecule provides the ability to administer said RNAi molecule to specific cell types, such as hepatocytes. For example, the asialoglycoprotein receptor (ASGPr) (Wu and Wu, 1987, J. Biol. Chem. 262:4429) is unique to hepatocytes and binds branched galactose-terminal glycoproteins, such as asialoorosomucoid (ASOR). Binding of such glycoproteins or synthetic glycoconjugates to the receptor takes place with an affinity that strongly depends on the degree of branching of the oligosaccharide chain, for example, triatennary structures are bound with greater affinity than biatenarry or monoatennary chains (Baenziger and Fiete, 1980, Cell 22: 611; Connolly et al., 1982, J. Biol. Chem. 257:939). Lee and Lee (1987, Glycoconjugate J. 4:317) obtained this high specificity through the use of N-acetyl-D-galactosamine as the carbohydrate moiety, which has higher affinity for the receptor compared to galactose. This “clustering effect” has also been described for the binding and uptake of mannosyl-terminating glycoproteins or glycoconjugates (Ponpipom et al., 1981, J. Med. Chem. 24: 1388). The use of galactose and galactosamine based conjugates to transport exogenous compounds across cell membranes can provide a targeted delivery approach to the treatment of liver disease. The use of bioconjugates can also provide a reduction in the required dose of therapeutic compounds required for treatment. Furthermore, therapeutic bioavailability, pharmacodynamics, and pharmacokinetic parameters can be modulated through the use of bioconjugates of this disclosure

Conjugate molecules described herein can be attached to a single-stranded RNAi molecule via non-nucleic acid linkers that are biodegradable. The term “biodegradable linker,” as used in this context, refers to a non-nucleic acid linker molecule that is designed as a biodegradable linker to connect one molecule to another molecule, for example, connecting a conjugate molecule to a single-stranded RNAi molecule of the invention. The biodegradable linker is designed such that its stability can be modulated for a particular purpose, such as delivery to a particular tissue or cell type. The term “biodegradable,” as used herein, refers to degradation in a biological system, for example enzymatic degradation or chemical degradation.

In one embodiment, a single-stranded RNAi molecule of the invention comprises an internal spacer portion comprising one or more non-nucleotide spacer portions, wherein said one or more non-nucleotide spacer portions (e.g., S1 or S2 within Formula III and IV) comprise or consist of a non-nucleotide spacer selected from the group consisting of a C3, a C6, a C9, and a C12 aliphatic spacer. The number after the “C” indicates the number of carbon atoms in the core spacer structure (e.g., if unsubstituted with additional chemical moieties). Said spacers can be alkyl, alkenyl, or alkynyl groups. Said spacers can also contain phosphoramidite moieties to facilitate covalent linkage to the phosphate backbone of the nucleotide portions of the molecule. In one embodiment, the spacer (S) portion is a C3 phosphoramidite spacer. In another embodiment, the spacer is a C6 phosphoramidite spacer. In a further embodiment, the C3, C6, C9, or C12 spacers are optionally substituted (e.g., with a targeting moiety).

One or more or all of the nucleotides within the nucleotide portions of a single-stranded RNAi molecule of the disclosure may be ribonucleotides, modified ribonucleotides, or suitable nucleotide analogs. Incorporation of nucleotide analogs, such as various known sugar, base, and backbone modifications, and LNA monomer units into disrupted strands may significantly enhance serum stability and prolong target knockdown or expression regulatory effects. The single-stranded RNA molecules of the present invention can functionally accommodate and are compatible with various chemical modifications to varying degrees. For example, from 5% to 100% of the ribonucleotides of a single-stranded RNA molecule of the invention may be modified (e.g., 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% of the ribonucleotides of the single-stranded RNAi molecules of the invention may be chemically modified or are replaced with nucleotide analog residues). The improved properties conferred by the functionally compatible chemical modifications to the sugar, base and/or backbone, or by including suitable nucleotide analog residues, are of particular importance for application of these single-stranded RNAi molecules in vivo, for example, for use as a therapeutic agent or as a functional genomic tool.

In a further aspect, a single-stranded RNAi molecule of the invention, according to any of the embodiments herein, are capable of participating in RNAi against a RNA target, including an endogenous RNA target. In one embodiment, the endogenous RNA target is the target of a naturally-occurring miRNA. The inhibition of the RNA target may be achieved via the standard RNA-specific interference mechanism, including miRNA-dependent RNA interference. For example, the inhibition of a miRNA target may be by interaction (e.g., base-pairng, binding, etc.) with the untranslated mRNA region, with which a corresponding endogenous miRNA interacts, which effectuates the translational regulation of one or more downstream genes. Alternatively, the inhibition of a miRNA target may be achieved via a siRNA-like interference mechanism wherein the binding of the miRNA target by the single-stranded RNAi molecule of the invention that is a miRNA mimetic results in the cleavage of the untranslated miRNA target. The single-stranded RNAi molecules of the invention may also inhibit mRNA target via a siRNA-like interference mechanism where the binding of the mRNA target in the sequence coding region (rather than in the non-coding untranslated region) by the single-stranded RNAi molecule of the invention results in cleavage of an mRNA target coding sequence.

C. Substituted and/or Modified Single-Stranded RNAi Molecules

The introduction of substituted and modified nucleotides into single-stranded RNAi molecules of the invention provides a tool for overcoming potential limitations of in vivo stability and bioavailability inherent to native RNA molecules (i.e., having standard nucleotides) that are exogenously delivered. In certain embodiments, the use of substituted or modified single-stranded RNAi molecules of this disclosure can enable achievement of a given therapeutic effect at a lower dose since these molecules may be designed to have an increased half-life in a subject or biological samples (e.g., serum). Furthermore, certain substitutions or modifications can be used to improve the bioavailability of single-stranded RNAi molecules by targeting particular cells or tissues or improving cellular uptake of the single-stranded RNAi molecules. Therefore, even if the activity of a single-stranded RNAi molecule of this disclosure is somewhat reduced (e.g., by less than about 20%, or 30%, or even 40%) as compared to an unmodified or unsubstituted RNAi molecule of the same structure, the overall activity of the substituted or modified RNAi molecule can be greater than that of its native counterpart due to improved stability or delivery of the molecule. Substituted and/or modified single-stranded RNAi molecules can also minimize the possibility of activating an interferon response in, for example, humans.

In certain embodiments, single-stranded RNAi molecules of the invention comprise ribonucleotides at about 5% to about 95% of the nucleotide positions. For example, from one to all (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 26, or 27) of the ribonucleotides of the single-stranded RNAi molecules of the invention can be modified.

In related embodiments, a single-stranded RNAi molecule according to the instant disclosure comprises one or more natural or synthetic non-standard nucleoside. In related embodiments, the non-standard nucleoside is one or more deoxyuridine, L- or D-locked nucleic acid (LNA) molecule (e.g., a 5-methyluridine LNA) or substituted LNA (e.g., having a pyrene), or a universal-binding nucleotide, or a G clamp, or any combination thereof. In certain embodiments, the universal-binding nucleotide can be C-phenyl, C-naphthyl, inosine, azole carboxamide, 1-β-D-ribofuranosyl-4-nitro indole, 1-β-D-ribofuranosyl-5-nitroindole, 1-β-D-ribofuranosyl-6-nitroindole, or 1-β-D-ribofuranosyl-3-nitropyrrole.

Substituted or modified nucleotides, which can be present in the single-stranded RNAi molecules of the invention, comprise modified or substituted nucleotides having characteristics similar to natural or standard ribonucleotides. For example, this disclosure features single-stranded RNAi molecules comprising nucleotides having a Northern conformation (see, e.g., Northern pseudorotation cycle, Saenger, Springer-Verlag ed., 1984), which are known to potentially impart resistant to nuclease degradation while maintaining the capacity to mediate RNAi, at least when applied to siRNA molecules. Exemplary nucleotides having a Northern configuration include locked nucleic acid (LNA) nucleotides (e.g., 2′-O, 4′-C-methylene-(D-ribofuranosyl) nucleotides), 2′-methoxyethyl (MOE) nucleotides, 2′-methyl-thio-ethyl, 2′-deoxy-2′-fluoro nucleotides, 2′-deoxy-2′-chloro nucleotides, 2′-azido nucleotides, 5-methyluridines, or 2′-O-methyl nucleotides). In any of these embodiments, one or more substituted or modified nucleotides can be a G clamp (e.g., a cytosine analog that forms an additional hydrogen bond to guanine, such as 9-(aminoethoxy)phenoxazine). See, e.g., Lin and Mateucci, 1998, J. Am. Chem. Soc. 720:8531.

In certain embodiments, the 5′-terminal end of single-stranded RNAi molecules of the invention is phosphorylated. In any of the embodiments of single-stranded RNAi molecules described herein, the molecule can further comprise a terminal phosphate group, such as a 5′-phosphate (see Martinez et al., 2002, Cell 110:563; Schwarz et al., 2002, Mole. Cell 70:537) or a 5′3′-diphosphate.

In another aspect, a single-stranded RNAi molecule of the invention comprises one or more 5′- and/or a 3′-cap structure at the terminal ends of the molecule. By “cap structure” is meant chemical modifications, which have been incorporated into the ends of oligonucleotide (see, for example, Matulic-Adamic et al., U.S. Pat. No. 5,998,203, incorporated by reference herein). These terminal modifications can protect certain nucleic acid molecules from exonuclease degradation, and can impart certain advantages in delivery and/or cellular localization. In non-limiting examples: a suitable 5′-cap can be one selected from the group comprising inverted abasic residue (moiety); 4′,5′-methylene nucleotide; 1-(beta-D-erythrofuranosyl) nucleotide, 4′-thio nucleotide; carbocyclic nucleotide; 1,5-anhydrohexitol nucleotide; L-nucleotides; alpha-nucleotides; modified base nucleotide; phosphorodithioate linkage; threo-pentofuranosyl nucleotide; acyclic 3′,4′-seco nucleotide; acyclic 3,4-dihydroxybutyl nucleotide; acyclic 3,5-dihydroxypentyl nucleotide, 3′-3′-inverted nucleotide moiety; 3′-3′-inverted abasic moiety; 3′-2′-inverted nucleotide moiety; 3′-2′-inverted abasic moiety; 1,4-butanediol phosphate; 3′-phosphoramidate; hexylphosphate; aminohexyl phosphate; 3′-phosphate; 3′-phosphorothioate; phosphorodithioate; or bridging or non-bridging methylphosphonate moiety.

In another non-limiting example, a suitable 3′-cap can be selected from a group comprising, 4′,5′-methylene nucleotide; 1-(beta-D-erythrofuranosyl) nucleotide; 4′-thio nucleotide, carbocyclic nucleotide; 5′-amino-alkyl phosphate; 1,3-diamino-2-propyl phosphate; 3-aminopropyl phosphate; 6-aminohexyl phosphate; 1,2-aminododecyl phosphate; hydroxypropyl phosphate; 1,5-anhydrohexitol nucleotide; L-nucleotide; alpha-nucleotide; modified base nucleotide; phosphorodithioate; threo-pentofuranosyl nucleotide; acyclic 3′,4′-seco nucleotide; 3,4-dihydroxybutyl nucleotide; 3,5-dihydroxypentyl nucleotide, 5′-5′-inverted nucleotide moiety; 5′-5′-inverted abasic moiety; 5′-phosphoramidate; 5′-phosphorothioate; 1,4-butanediol phosphate; 5′-amino; bridging and/or non-bridging 5′-phosphoramidate, phosphorothioate and/or phosphorodithioate, bridging or non bridging methylphosphonate and 5′-mercapto moieties. For more details, see Beaucage and Iyer, 1993, Tetrahedron 49:1925, which is incorporated by reference herein.

In certain embodiments, this disclosure features modified single-stranded RNAi molecules comprising phosphate backbone modifications, including, for example, one or more phosphorothioate, phosphorodithioate, methylphosphonate, phosphotriester, morpholino, amidate carbamate, carboxymethyl, acetamidate, polyamide, sulfonate, sulfonamide, sulfamate, formacetal, thioformacetal, or alkylsilyl, substitutions. For a review of oligonucleotide backbone modifications, see Hunziker and Leumann, 1995, Nucleic Acid Analogues: Synthesis and Properties, in Modern Synthetic Methods, VCH, 331; Mesmaeker et al., 1994, ACS 24-39.

In further embodiments, a single-stranded RNAi molecule comprises one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26) 2′-sugar substitutions, such as a 2′-deoxy, 2′-O-2-methoxyethyl, 2′-O-methoxyethyl, 2′-O-methyl, 2′-halogen (e.g., 2′-fluoro), 2′-O-allyl, or the like, or any combination thereof. In still further embodiments, a single-stranded RNAi molecule comprises a terminal cap substituent at one or both terminal ends, such as, for example, an alkyl, abasic, deoxy abasic, glyceryl, dinucleotide, acyclic nucleotide, inverted deoxynucleotide moiety, or any combination thereof. In certain embodiments, at least one 5′-terminal-end ribonucleotide has a 2′-sugar substitution.

In other embodiments, a single-stranded RNAi molecule comprises one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26) substitutions in the sugar backbone, including any combination of ribosyl, 2′-deoxyribosyl, a tetrofuranosyl (e.g., L-α-threofuranosyl), a hexopyranosyl (e.g., β-allopyranosyl, β-altropyranosyl and β-glucopyranosyl), a pentopyranosyl (e.g., β-ribopyranosyl, α-lyxopyranosyl, β-xylopyranosyl and α-arabinopyranosyl), a carbocyclic analog, a pyranose, a furanose, a morpholino, or analogs or derivatives thereof.

In yet other embodiments, a single-stranded RNAi molecule comprises at least one (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26) modified internucleoside linkage, such as independently a phosphorothioate, chiral phosphorothioate, phosphorodithioate, phosphotriester, aminoalkylphosphotriester, methyl phosphonate, alkyl phosphonate, 3′-alkylene phosphonate, 5′-alkylene phosphonate, chiral phosphonate, phosphonoacetate, thiophosphonoacetate, phosphinate, phosphoramidate, 3′-amino phosphoramidate, aminoalkylphosphoramidate, thionophosphoramidate, thionoalkylphosphonate, thionoalkylphosphotriester, selenophosphate, boranophosphate linkage, or any combination thereof.

A single-stranded RNAi molecule can comprise one or more modified internucleotide linkages at the 3′-terminal end, the 5′-terminal end, or both of the 3′-terminal and 5′-terminal ends of the molecule. In one embodiment, a single-stranded RNAi molecule of the invention has one modified internucleotide linkage at the 3′-terminal end, such as a phosphorothioate linkage. An exemplary single-stranded RNAi molecule comprises about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more phosphorothioate internucleotide linkages. A further exemplary single-stranded RNAi molecule comprises about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more consecutive phosphorothioate internucleotide linkages at, for example, the 5′-terminal end of the molecule. In yet another exemplary single-stranded RNAi molecule, there can be one or more pyrimidine phosphorothioate internucleotide linkages. In a further exemplary single-stranded RNAi molecule, there can be one or more purine phosphorothioate internucleotide linkages.

Many exemplary modified nucleotide bases or analogs thereof useful in single-stranded RNAi molecules of the instant disclosure include 5-methylcytosine; 5-hydroxymethylcytosine; xanthine; hypoxanthine; 2-aminoadenine; 6-methyl, 2-propyl, or other alkyl derivatives of adenine and guanine; 8-substituted adenines and guanines (e.g., 8-aza, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl, or the like); 7-methyl, 7-deaza, and 3-deaza adenines and guanines; 2-thiouracil; 2-thiothymine; 2-thiocytosine; 5-methyl, 5-propynyl, 5-halo (e.g., 5-bromo or 5-fluoro), 5-trifluoromethyl, or other 5-substituted uracils and cytosines; and 6-azouracil. Further useful nucleotide bases can be found in Kurreck, 2003, Eur. J. Biochem. 270:1628; Herdewijn, 2000, Guide Nucleic Acid Develop. 10:297; Concise Encyclopedia of Polymer Science and Engineering, pp. 858-859, Kroschwitz, J. L, ed. John Wiley & Sons, 1990; U.S. Pat. No. 3,687,808, and similar references, all of which are incorporated by reference herein.

Certain substituted or modified nucleotide base moieties are also contemplated. These include 5-substituted pyrimidines; 6-azapyrimidines; and N-2, N-6, or 0-6 substituted purines (e.g., 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine). Further, for example, 5-methyluridine and 5-methylcytosine substitutions are known to increase nucleic acid duplex stability, which can be combined with 2′-sugar modifications (e.g., 2′-O-methyl or 2′-methoxyethyl) or internucleoside linkages (e.g., phosphorothioate) that provide the desired nuclease resistance to the modified or substituted single-stranded RNAi molecule.

In further embodiments, at least one pyrimidine of a single-stranded RNAi molecule of the invention is a locked nucleic acid (LNA) in the form of a bicyclic sugar. In a related embodiment, the LNA comprises a base substitution, such as a 5-methyluridine LNA or 2-thio-5-methyluridine LNA. In further embodiments, a ribose of the pyrimidine nucleoside or the internucleoside linkage can be optionally modified.

In any of these embodiments, one or more substituted or modified nucleotides can be a G clamp (e.g., a cytosine analog that forms an additional hydrogen bond to guanine, such as 9-(aminoethoxy) phenoxazine). See, e.g., Lin and Mateucci, 1998, Nucleic Acids Res. 19:3111.

In any of the embodiments described herein, a single-stranded RNAi molecule may include multiple types of modifications. For example, a single-stranded RNAi molecule having at least one ribothymidine or 2-thioribothymidine can further comprise at least one LNA, 2′-methoxy, 2′-fluoro, 2′-deoxy, phosphorothioate linkage, an inverted base terminal cap, or any combination thereof. In certain exemplary embodiments, a single-stranded RNAi molecule can comprise one or more or all uridines substituted with ribothymidine and have up to about 75% LNA substitutions. In other exemplary embodiments, a single-stranded RNAi molecule can comprise from one or more or all uridines substituted with ribothymidine and have up to about 25% 2′-methoxy substitutions. In still other exemplary embodiments, a single-stranded RNAi molecule can comprise one or more or all uridines substituted with ribothymidine and have up to about 100% 2′-fluoro substitutions.

Within certain aspects, the present disclosure also provides single-stranded RNAi molecules comprising one or more universal base nucleotides. The term “universal base” as used herein refers to nucleotide base analogs that form base pairs or hydrogen bonded nucleotide pairs with more than one types of nucleotides. Non-limiting examples of universal bases include C-phenyl, C-naphthyl and other aromatic derivatives, inosine, azole carboxyamides, and nitroazole derivatives such as 3-nitropyrrole, 4-nitroindole, 5-nitroindole, and 6-nitroindole as known in the art (see, e.g., Loakes, 2001, Nucleic Acids Research 29:2437-2447). In certain aspects, a single-stranded RNAi molecule disclosed herein can include about 1 to about 10 universal base nucleotides, so long as the resulting RNAi molecule remains capable of modulating one or more of its endogenous targets.

D. Synthesis of Single-Stranded RNAi Molecules

Exemplary molecules of the instant disclosure can be obtained using a number of techniques known to those of skill in the art. For example, the RNAi molecules of the invention can be chemically synthesized, recombinantly produced (e.g., encoded by plasmid), or a combination thereof.

Oligonucleotides or individual contiguous stretches of nucleotides (e.g., certain modified oligonucleotides or portions of oligonucleotides lacking ribonucleotides) are synthesized using protocols known in the art, for example, as described in Caruthers et al., 1992, Methods in Enzymol. 211:3; Thompson et al, PCT Publication No. WO 99/54459; Wincott et al., 1995, Nucleic Acids Res. 23:2677; Wincott et al., 1997, Methods Mol. Bio. 74:59; Brennan et al., 1998, Biotechnol. Bioeng. 67:33; and Brennan, U.S. Pat. No. 6,001,311. The synthesis of oligonucleotides makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5′-end, and phosphoramidites at the 3′-end. Synthesis of RNA without modifications, including certain single-stranded RNAi molecules thereof of this disclosure, can be made using the procedure as described in Usman et al., 1987, J. Am. Chem. Soc. 109:7845; Scaringe et al., 1990, Nucleic Acids Res. 18:5433; and Wincott et al., 1995, Nucleic Acids Res. 23:2677; and Wincott et al., 1997, Methods Mol. Bio. 74:59. In certain embodiments, the nucleotide portions of the single-stranded RNAi molecules of the present disclosure can be synthesized separately and joined together with the non-nucleotide spacer portions post-synthetically, for example, by ligation (Moore et al., 1992, Science 256:9923; Draper et al., PCT Publication No. WO 93/23569; Shabarova et al., 1991, Nucleic Acids Res. 19:4247; Bellon et al., 1997, Nucleosides & Nucleotides 16:951; Bellon et al., 1997, Bioconjugate Chem. 8:204). In a further embodiment, the nucleotide portion of a single-stranded RNAi molecule of this disclosure can be made as single or multiple transcription products expressed by a polynucleotide (DNA or RNA) vector encoding one or more contiguous stretches of RNAs and directing their expression within host cells. The nucleotide portions are then isolated and joined by ligation with a non-nucleotide spacer portion.

In some embodiments, pol III based constructs are used to express nucleic acid molecules of the invention. Transcription of the single-stranded RNAi molecule sequences can be driven from a promoter for eukaryotic RNA polymerase I (pol I), RNA polymerase II (pol II), or RNA polymerase III (pol III). (see for example, Thompson, U.S. Pat. Nos. 5,902,880 and 6,146,886). (See also, Izant and Weintraub, 1985, Science, 229, 345; McGarry and Lindquist, 1986, Proc. Natl. Acad. Sci., USA 83, 399; Scanlon et al., 1991, Proc. Natl. Acad. Sci. USA, 88, 10591-5; Kashani-Sabet et al., 1992, Antisense Res. Dev., 2, 3-15; Dropulic et al., 1992, J. Virol., 66, 1432-41; Weerasinghe et al., 1991, J. Virol., 65, 5531-4; Ojwang et al., 1992, Proc. Natl. Acad. Sci. USA, 89, 10802-6; Chen et al., 1992, Nucleic Acids Res., 20, 4581-9; Sarver et al., 1990 Science, 247, 1222-1225; Thompson et al., 1995, Nucleic Acids Res., 23, 2259; Good et al., 1997, Gene Therapy, 4, 45. Transcripts from pol II or pol III promoters are expressed at high levels in all cells; the levels of a given pol II promoter in a given cell type depends on the nature of the gene regulatory sequences (enhancers, silencers, etc.) present nearby. Prokaryotic RNA polymerase promoters are also used, providing that the prokaryotic RNA polymerase enzyme is expressed in the appropriate cells (Elroy-Stein and Moss, 1990, Proc. Natl. Acad. Sci. USA, 87, 6743-7; Gao and Huang 1993, Nucleic Acids Res., 21, 2867-72; Lieber et al., 1993, Methods Enzymol., 217, 47-66; Zhou et al., 1990, Mol. Cell. Biol., 10, 4529-37). Several investigators have demonstrated that nucleic acid molecules expressed from such promoters can function in mammalian cells (e.g. Kashani-Sabet et al., 1992, Antisense Res. Dev., 2, 3-15; Ojwang et al., 1992, Proc. Natl. Acad. Sci. USA, 89, 10802-6; Chen et al., 1992, Nucleic Acids Res., 20, 4581-9; Yu et al., 1993, Proc. Natl. Acad. Sci. USA, 90, 6340-4; L'Huillier et al., 1992, EMBO J., 11, 4411-8; Lisziewicz et al., 1993, Proc. Natl. Acad. Sci. U.S.A, 90, 8000-4; Thompson et al., 1995, Nucleic Acids Res., 23, 2259; Sullenger & Cech, 1993, Science, 262, 1566). More specifically, transcription units such as the ones derived from genes encoding U6 small nuclear (snRNA), transfer RNA (tRNA) and adenovirus VA RNA are useful in generating high concentrations of desired RNA molecules (Thompson et al., supra; Couture and Stinchcomb, 1996, supra; Noonberg et al., 1994, Nucleic Acid Res., 22, 2830; Noonberg et al., U.S. Pat. No. 5,624,803; Good et al., 1997, Gene Ther., 4, 45; Beigelman et al., International PCT Publication No. WO 96/18736. The above transcription units can be incorporated into a variety of vectors for introduction into mammalian cells, including but not restricted to, plasmid DNA vectors, viral DNA vectors (such as adenovirus or adeno-associated virus vectors), or viral RNA vectors (such as retroviral or alphavirus vectors) (for a review see Couture and Stinchcomb, 1996, supra).

Chemically synthesizing nucleic acid molecules with substitutions or modifications (base, sugar, phosphate, or any combination thereof) can impart resistance to degradation by serum ribonucleases, which may lead to increased potency and other pharmacological and therapeutic benefits. See, e.g., Eckstein et al., PCT Publication No. WO 92/07065; Perrault et al., 1990, Nature 344:565; Pieken et al., 1991, Science 253:314; Usman and Cedergren, 1992, Trends in Biochem. Sci. 77:334; Usman et al., 1994, Nucleic Acids Symp. Ser. 31:163; Beigelman et al., 1995, J. Biol Chem. 270:25702; Burlina et al., 1997, Bioorg. Med. Chem. 5:1999; Karpeisky et al., 1998, Tetrahedron Lett. 39:1131; Earnshaw and Gait, 1998, Biopolymers (Nucleic Acid Sciences) 48:39; Verma and Eckstein, 1998, Annu. Rev. Biochem. 67:99; Herdewijn, 2000, Guide Nucleic Acid Drug Dev. 10:291; Kurreck, 2003, Eur. J. Biochem. 270:1628; Dorsett and Tuschl, 2004, Nature Rev. Drug Discov. 3:318; Rossi et al., PCT Publication No. WO 91/03162; Usman et al., PCT Publication No. WO 93/15187; Beigelman et al., PCT Publication No. WO 97/26270; Woolf et al., PCT Publication No. WO 98/13526; Sproat, U.S. Pat. No. 5,334,711; Usman et al., U.S. Pat. No. 5,627,053; Beigelman et al., U.S. Pat. No. 5,716,824; Otvos et al., U.S. Pat. No. 5,767,264; Gold et al., U.S. Pat. No. 6,300,074. Each of the above references discloses various substitutions and chemical modifications to the base, phosphate, or sugar moieties of nucleic acid molecules, which can be used in the single-stranded RNAi molecules described herein.

E. Methods for Designing a Single-Stranded RNAi Molecule

As described herein, the single-stranded RNA molecules of the present invention are capable of inhibiting the expression of a target sequence via an RNAi mechanism. In one embodiment, the single-stranded RNAi molecules can be designed based on a previously identified RNAi agent possessing a desired knockdown function (e.g., siRNA, miRNA). For example, if a single-stranded RNAi molecule of the present invention is a miRNA mimetic, it is derived from a corresponding, naturally-occurring miRNA molecule (see Table 1) or an analog thereof (e.g., a chemically modified form). As of the filing date of the present application, over 3000 miRNA molecules endogenous to a variety of species can be found in publically available databases (see, e.g., the publicly available miRBase sequence database as described in Griffith-Jones et al., 2004, Nucleic Acids Research 32:D109-D111 and Griffith-Jones et al., 2006, Nucleic Acids Research 34:D 140-D144, accessible on the World Wide Web at the Wellcome Trust Sanger Institute website). Table 1 herein contains a list of 1090 mature human miRNA sequences (SEQ ID NO: 1-1090). In another example, a single-stranded RNAi molecule of the present invention may be derived from a previously identified siRNA either known to inhibit expression of a target sequence of choice or has the potential of inhibiting expression of a target mRNA sequence. Specifically, a single-stranded RNAi molecule that is derived from a previously identified RNAi molecule (i.e., the reference RNAi molecule) can be designed by introducing one or more internal, non-nucleotide spacers portions within the guide strand of the reference RNAi molecule. In another embodiment, the single-stranded RNAi molecules can be designed de novo (i.e., not based on a known RNAi agent) for the purpose of knocking down expression of a particular target sequence.

The RNAi activity of a given single-stranded RNAi molecule of the invention can be measured using known methods, such as those described generally in Fire et al., PCT Publication No. WO99/32619, and as described in the Examples section infra. In some embodiments, the instant specification provides methods for selecting more efficacious single-stranded RNAi molecule designs by using one or more reporter gene constructs comprising a constitutive promoter, such as a cytomegalovirus (CMV) or phosphoglycerate kinase (PGK) promoter, operably fused to, and capable of altering the expression of one or more reporter genes, such as a luciferase, chloramphenicol (CAT), or β-galactosidase, which, in turn, is operably fused in-frame to a portion of the target sequence that is whole or partially complementary to the ssRNAi to be tested. These reporter gene expression constructs may be co-transfected with one or more ssRNAi molecules and a control (e.g., corresponding miRNA mimetic that does not contain the internal non-nucleotide spacer). The capacity of a given ssRNAi molecule to mediate RNAi of a target mRNA may be determined by comparing the measured reporter gene activity in cells transfected with the ssRNAi molecule and the activity in cells transfected with a negative control (i.e., in cells not transfected with the ssRNAi molecule) and a positive control (e.g., in cells transfected with the corresponding miRNA mimetic that does not contain the internal non-nucleotide spacer). The ssRNAi molecules having at least 20% or more, preferably at least 40% or more, or 60% or more, or 80% or more, of the activity of their corresponding RNAi molecule, for example, that do not contain internal non-nucleotide spacers, are selected.

A person of skill in the art can screen single-stranded RNAi molecules of this disclosure containing various non-nucleotide spacers to determine which of molecules possess improved properties (e.g., pharmacokinetic profile, bioavailability, stability) while maintaining the ability to mediate RNAi in, for example, an animal model as described herein or generally known in the art. Similarly, a person of skill in the art can also screen single-stranded RNAi molecules of this disclosure having various conjugates to determine which of the RNAi molecule-conjugate complexes possess improved properties while maintaining the ability to mediate RNAi.

F. Compositions and Methods of Use

As set forth herein, single-stranded RNA molecules of the invention are RNAi agents preferably capable of participating in the cellular RNAi pathway or otherwise capable of modulating the same or related pathway(s) and resulting in the inhibition of a target gene associated with a pathological or diseased condition. In the case of a single-stranded RNA molecule that represents a miRNA mimetic, the ssRNAi molecule is designed to supplement or take the place of a corresponding, naturally-occurring miRNA, the reduced or otherwise unsuitably low levels of which have been associated with pathological or diseased conditions. The single-stranded RNAi molecules of the invention thus are useful reagents, which can be used in methods for a variety of therapeutic, diagnostic, target validation, genomic discovery, genetic engineering, and pharmacogenomic applications.

A single-stranded RNA molecule of the invention can be introduced to a cell, tissue, organism, in vitro system, or in vivo system to mediate RNAi against a target sequence. That target sequence may be an endogenous target gene or sequence. In one embodiment, the single-stranded RNAi molecules of the invention can be used for treating organisms having a disease characterized by the undesired production of a protein.

In the case of a single-stranded RNAi molecule of the invention that is a miRNA mimetic, the target sequence is the target of a corresponding, naturally-occurring miRNA. In such a case, the single-stranded miRNA mimetic may regulate a number of genes, for example, downstream from its mRNA target, whose expression levels are associated with or otherwise regulated by the corresponding, naturally-occurring miRNA. Because aberrant expression levels of certain naturally-occurring miRNAs have been implicated in various human ailments, including, but not limited to, hyperproliferative, angiogenic, or inflammatory diseases, states, or adverse conditions, the single-stranded miRNA mimetics of the present invention can offer valuable therapeutic opportunities. In this context, a single-stranded miRNA mimetic of this disclosure can regulate (e.g., knockdown or up-regulate) expression of one or more downstream genes of its corresponding endogenous miRNA, such that prevention, alleviation, or reduction of the severity or recurrence of one or more associated disease symptoms can be achieved. Alternatively, for various distinct disease models in which expression of one or more target mRNAs are not necessarily reduced or at a lower-than-normal level as a consequence of diseases or other adverse conditions, introducing exogenous miRNA mimetics, such as one or more single-stranded miRNA mimetics of the invention, may nonetheless result in a therapeutic result by affecting the expression levels of genes associated with the disease pathway.

A single-stranded RNAi molecule of invention can also act similar to a siRNA molecule in targeting the coding region of a target gene, inhibiting the expression that gene and, thus, reducing protein production. The protein that would have been produced if not for introduction of the single-stranded RNAi molecule may be associated with a pathological or diseased condition (e.g., cancer).

In accordance with this disclosure herein, a single-stranded RNAi molecule of the invention, compositions thereof, and methods for inhibiting expression of one or more corresponding target mRNAs in a cell or organism are provided. This disclosure provides methods and single-stranded RNAi molecule compositions for treating a subject, including a human cell, tissue or individual.

(i) Pharmaceutical Compositions and Formulations

The present disclosure includes single-stranded RNAi molecule compositions prepared for storage or administration that include a pharmaceutically effective amount of a desired RNAi molecule in a pharmaceutically acceptable carrier or diluent. The single-stranded RNAi molecule compositions of the disclosure can be effectively employed as pharmaceutically-acceptable formulations. Pharmaceutically-acceptable formulations prevent, alter the occurrence or severity of, or treat (alleviate one or more symptom(s) to a detectable or measurable extent) a disease state or other adverse condition in a subject. Thus, a pharmaceutical composition or formulation refers to a composition or formulation in a form suitable for administration into a cell, or a subject such as a human (e.g., systemic administration). The pharmaceutical compositions of the present disclosure are formulated to allow the single-stranded RNAi molecule(s) contained therein to be bioavailable upon administration to a subject.

In certain embodiments, pharmaceutical compositions of this disclosure can optionally include preservatives, antioxidants, stabilizers, dyes, flavoring agents, or any combination thereof. Exemplary preservatives include sodium benzoate, esters of p-hydroxybenzoic acid, and sorbic acid. A pharmaceutically acceptable formulation includes salts of the above compounds, for example, acid addition salts, such as salts of hydrochloric acid, hydrobromic acid, acetic acid, or benzene sulfonic acid. Acceptable carriers or diluents for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co., A. R. Gennaro edit., 21st Edition, 2005.

In certain embodiments, aqueous suspensions containing one or more single-stranded RNAi molecules of the invention can be prepared in an admixture with suitable excipients, such as suspending agents or dispersing or wetting agents. Exemplary suspending agents include sodium carboxymethylcellulose, methylcellulose, hydropropyl-methylcellulose, sodium alginate, polyvinylpyrrolidone, gum tragacanth and gum acacia. Representative dispersing or wetting agents include naturally-occurring phosphatides (e.g., lecithin), condensation products of an alkylene oxide with fatty acids (e.g., polyoxyethylene stearate), condensation products of ethylene oxide with long chain aliphatic alcohols (e.g., heptadecaethyleneoxycetanol), condensation products of ethylene oxide with partial esters derived from fatty acids and hexitol (e.g., polyoxyethylene sorbitol monooleate), or condensation products of ethylene oxide with partial esters derived from fatty acids and hexitol anhydrides (e.g., polyethylene sorbitan monooleate). In certain embodiments, the aqueous suspensions can optionally contain one or more preservatives (e.g., ethyl or w-propyl-p-hydroxybenzoate), one or more coloring agents, one or more flavoring agents, or one or more sweetening agents (e.g., sucrose, saccharin). In additional embodiments, dispersible powders and granules suitable for preparation of an aqueous suspension comprising one or more single-stranded RNAi molecules of the invention can be prepared by the addition of water with the single-stranded RNAi molecules in admixture with a dispersing or wetting agent, suspending agent and optionally one or more preservative, coloring agent, flavoring agent, or sweetening agent.

In further embodiments, a single-stranded RNAi molecule of this disclosure can be formulated as oily suspensions or emulsions (e.g., oil-in-water) by suspending the ssRNAi in, for example, a vegetable oil (e.g., arachis oil, olive oil, sesame oil or coconut oil) or a mineral oil (e.g., liquid paraffin). Suitable emulsifying agents can be naturally-occurring gums (e.g., gum acacia or gum tragacanth), naturally-occurring phosphatides (e.g., soy bean, lecithin, esters or partial esters derived from fatty acids and hexitol), anhydrides (e.g., sorbitan monooleate), or condensation products of partial esters with ethylene oxide (e.g., polyoxyethylene sorbitan monooleate). In certain embodiments, the oily suspensions or emulsions can optionally contain a thickening agent, such as beeswax, hard paraffin or cetyl alcohol. In related embodiments, sweetening agents and flavoring agents can optionally be added to provide palatable oral preparations. In yet other embodiments, these compositions can be preserved by the optionally adding an anti-oxidant, such as ascorbic acid.

In further embodiments, single-stranded RNAi molecules can be formulated as syrups and elixirs with sweetening agents (e.g., glycerol, propylene glycol, sorbitol, glucose or sucrose). Such formulations can also contain a demulcent, preservative, flavoring, coloring agent, or any combination thereof.

In other embodiments, pharmaceutical compositions comprising a single-stranded RNAi molecule of the invention can be in the form of a sterile, injectable aqueous or oleaginous suspension. The sterile, injectable preparation can also be a sterile, injectable solution or suspension in a non-toxic, parenterally-acceptable diluent or solvent (e.g., as a solution in 1,3-butanediol). Among the exemplary acceptable vehicles and solvents useful in the compositions of this disclosure is water, Ringer's solution, or isotonic sodium chloride solution. In addition, sterile, fixed oils may be employed as a solvent or suspending medium. For this purpose, any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid find use in the preparation of parenteral formulations.

The single-stranded RNAi molecules of the invention can be administered directly, or can be complexed, for example, with cationic lipids or packaged within liposomes, or otherwise delivered to target cells or tissues. Methods for the delivery of nucleic acid molecules are described in Akhtar et al., 1992, Trends Cell Bio., 2:139; Delivery Strategies for Antisense Oligonucleotide Therapeutics, ed. Akhtar, 1995; Maurer et al., 1999, Mol. Membr. Biol. 16:129-140; Hofland and Huang, 1999, Handb. Exp. Pharmacol. 137:165-192; and Lee et al., 2000, ACS Symp. Ser. 752:184-192. Beigelman et al., U.S. Pat. No. 6,395,713 and Sullivan et al., PCT WO 94/02595 further describe the general methods for delivery of nucleic acid molecules. These protocols can be utilized for the delivery of virtually any nucleic acid molecule. Nucleic acid molecules can be administered to cells by a variety of methods known to those of skill in the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other vehicles, such as biodegradable polymers, hydrogels, cyclodextrins (see for example, Gonzalez et al., 1999, Bioconjugate Chem., 10, 1068-1074; Wang et al., International PCT Publication Nos. WO 03/47518 and WO 03/46185), poly(lactic-co-glycolic)acid (PLGA) and PLCA microspheres (see for example U.S. Pat. No. 6,447,796 and US Patent Application Publication No. US 2002130430), biodegradable nanocapsules, and bioadhesive microspheres, or by proteinaceous vectors (O'Hare and Normand, International PCT Publication No. WO 00/53722).

(ii) Carrier/Delivery Systems

In one aspect, the present invention provides carrier systems containing the single-stranded RNAi molecules described herein. In some embodiments, the carrier system is a lipid-based carrier system, cationic lipid, or liposome nucleic acid complexes, a liposome, a micelle, a virosome, a lipid nanoparticle or a mixture thereof. In other embodiments, the carrier system is a polymer-based carrier system such as a cationic polymer-nucleic acid complex. In additional embodiments, the carrier system is a cyclodextrin-based carrier system such as a cyclodextrin polymer-nucleic acid complex. In further embodiments, the carrier system is a protein-based carrier system such as a cationic peptide-nucleic acid complex. Preferably, the carrier system in a lipid nanoparticle (“LNP”) formulation.

In certain embodiments, the single-stranded RNAi molecules of the invention are formulated with a lipid nanoparticle composition such as is described in U.S. patent application Ser. Nos. 11/353,630, 11/586,102, 61/189,295, 61/204,878, 61/235,476, 61/249,807, and 61/298,022. In certain preferred embodiments, the ssRNAi molecules of the invention are formulated with a lipid nanoparticle composition comprising a cationic lipid/Cholesterol/PEG-C-DMA/DSPC in a 40/48/2/10 ratio or a cationic lipid/Cholesterol/PEG-DMG/DSPC in a 40/48/2/10 ratio. In certain other embodiments, the invention features a composition comprising a ssRNAi molecule of the invention formulated with any of the cationic lipid formulations described in U.S. Patent Application Nos. 61/189,295, 61/204,878, 61/235,476, 61/249,807, and 61/298,022.

Within certain embodiments of this disclosure, pharmaceutical compositions and methods are provided that feature the presence or administration of one or more single-stranded RNAi molecule, combined, complexed, or conjugated with functional moiety, optionally formulated with a pharmaceutically-acceptable carrier, such as a diluent, stabilizer, buffer, or the like. Such conjugates and/or complexes can be used to facilitate delivery of RNAi molecules into a biological system, such as a cell. The conjugates and complexes provided by the instant invention can impart therapeutic activity by transferring therapeutic compounds across cellular membranes, altering the pharmacokinetics, and/or modulating the localization of nucleic acid molecules of the invention. Non-limiting, examples of such conjugates are described in U.S. Publication Nos. US2008/0152661 A1 and US 2004/0162260 A1 (e.g., CDM-LBA, CDM-Pip-LBA, CDM-PEG, CDM-NAG, etc.) and U.S. patent application Ser. Nos. 10/427,160 and 10/201,394; and U.S. Pat. Nos. 6,528,631; 6,335,434; 6,235,886; 6,153,737; 5,214,136; and 5,138,045.

A single-stranded RNAi molecule of this disclosure can include a conjugate member on one or more of the nucleotides, at a terminal and/or internal position(s), and/or on the spacer portion of the molecule. The conjugate member can be, for example, a lipophile, a terpene, a protein binding agent, a vitamin, a carbohydrate, or a peptide. For example, the conjugate member can be naproxen, nitroindole (or another conjugate that contributes to stacking interactions), folate, ibuprofen, or a C5 pyrimidine linker. In other embodiments, the conjugate member is a glyceride lipid conjugate (e.g., a dialkyl glyceride derivatives), vitamin E conjugates, or thio-cholesterols. In various embodiments, polyethylene glycol (PEG) can be covalently attached to single-stranded RNAi molecules of the present invention. The attached PEG can be any molecular weight, preferably from about 100 to about 50,000 daltons (Da).

Within certain embodiments of this disclosure, pharmaceutical compositions and methods are provided that feature the presence or administration of one or more single-stranded RNAi molecule, combined, complexed, or conjugated with a polypeptide or peptide, optionally formulated with a pharmaceutically-acceptable carrier, such as a diluent, stabilizer, buffer, or the like. In certain embodiments, when peptide conjugate partners are used to enhance delivery of one or more single-stranded RNAi molecules of this disclosure into a target cell, or otherwise enhance stability or activity of the molecule when contacted with a biological sample. Exemplary peptide conjugate members for use within these aspects of this disclosure, include peptides PN27, PN28, PN29, PN58, PN61, PN73, PN158, PN159, PN173, PN182, PN202, PN204, PN250, PN361, PN365, PN404, PN453, and PN509 as described, for example, in U.S. Patent Application Publication Nos. 2006/0040882 and 2006/0014289, and U.S. Provisional Patent Application No. 60/939,578, which are all incorporated herein by reference.

In one embodiment, this disclosure provides compositions suitable for administering single-stranded RNAi molecules of this disclosure to specific cell types, such as hepatocytes. For example, the asialoglycoprotein receptor (ASGPr) (Wu and Wu, 1987, J. Biol. Chem. 262:4429) is unique to hepatocytes and binds branched galactose-terminal glycoproteins, such as asialoorosomucoid (ASOR). Binding of such glycoproteins or synthetic glycoconjugates to the receptor takes place with an affinity that strongly depends on the degree of branching of the oligosaccharide chain, for example, triatennary structures are bound with greater affinity than biatenarry or monoatennary chains (Baenziger and Fiete, 1980, Cell 22: 611; Connolly et al., 1982, J. Biol. Chem. 257:939). Lee and Lee (1987, Glycoconjugate J. 4:317) obtained this high specificity through the use of N-acetyl-D-galactosamine as the carbohydrate moiety, which has higher affinity for the receptor compared to galactose. This “clustering effect” has also been described for the binding and uptake of mannosyl-terminating glycoproteins or glycoconjugates (Ponpipom et al., 1981, J. Med. Chem. 24: 1388). The use of galactose and galactosamine based conjugates to transport exogenous compounds across cell membranes can provide a targeted delivery approach to the treatment of liver disease. The use of bioconjugates can also provide a reduction in the required dose of therapeutic compounds required for treatment. Furthermore, therapeutic bioavailability, pharmacodynamics, and pharmacokinetic parameters can be modulated through the use of bioconjugates of this disclosure.

In still another embodiment, a single-stranded RNAi molecule of the invention may be conjugated to a polypeptide and admixed with one or more non-cationic lipids or a combination of a non-cationic lipid and a cationic lipid to form a composition that enhances intracellular delivery of the RNAi molecule as compared to delivery resulting from contacting the target cells with a naked RNAi molecule without the lipids. In more detailed aspects of this disclosure, the mixture, complex or conjugate comprising a single-stranded RNAi molecule and a polypeptide can be optionally combined with (e.g., admixed or complexed with) a cationic lipid, such as Lipofectine™. To produce these compositions comprised of a polypeptide, a single-stranded RNAi molecule and a cationic lipid, the RNAi molecule and the polypeptide may be mixed together first in a suitable medium such as a cell culture medium, after which the cationic lipid is added to the mixture to form an RNAi molecule/delivery peptide/cationic lipid composition. Optionally, the peptide and cationic lipid can be mixed together first in a suitable medium such as a cell culture medium, followed by the addition of the single-stranded RNAi molecule to form the RNAi molecule/delivery peptide/cationic lipid composition.

This disclosure also features the use of single-stranded RNAi molecule compositions comprising surface-modified liposomes containing poly(ethylene glycol) lipids (PEG-modified, or long-circulating liposomes or stealth liposomes). These formulations may offer increased accumulation of drugs in target tissues (Lasic et al., 1995, Chem. Rev. 95:2601; Ishiwata et al., 1995, Chem. Pharm. Bull. 43:1005). Such liposomes have been shown to accumulate selectively in tumors, presumably by extravasation and capture in the neovascularized target tissues (Lasic et al., 1995, Science 267:1215; Oku et al., 1995, Biochim. Biophys. Acta 1238:86). The long-circulating liposomes enhance the pharmacokinetics and pharmacodynamics of nucleic acid molecules as compared to conventional cationic liposomes, which are known to accumulate in tissues of the mononuclear phagocytic system (MPS) (Liu et al., 1995, J. Biol. Chem. 42:24864; Choi et al., PCT Publication No. WO 96/10391; Ansell et al., PCT Publication No. WO 96/10390; Holland et al., PCT Publication No. WO 96/10392). Long-circulating liposomes may also provide additional protection from nuclease degradation as compared to cationic liposomes, in theory due to avoiding accumulation in metabolically aggressive MPS tissues, such as the liver and spleen.

In some embodiments, the RNAi molecules of the invention can also be formulated or complexed with polyethyleneimine and derivatives thereof, such as polyethyleneimine-polyethyleneglycol-N-acetylgalactosamine (PEI-PEG-GAL) or polyethyleneimine-polyethyleneglycol-tri-N-acetylgalactosamine (PEI-PEG-triGAL) derivatives. In one embodiment, the nucleic acid molecules of the invention are formulated as described in U.S. Patent Application Publication No. 20030077829.

In other embodiments, single-stranded RNAi molecules of the invention are complexed with membrane disruptive agents such as those described in U.S. Patent Application Publication No. 20010007666. In still other embodiments, the membrane disruptive agent or agents and the RNAi molecule are also complexed with a cationic lipid or helper lipid molecule, such as those lipids described in U.S. Pat. No. 6,235,310.

In certain embodiments, single-stranded RNAi molecules of the invention are complexed with delivery systems as described in U.S. Patent Application Publication Nos. 2003077829; 20050287551; 20050164220; 20050191627; 20050118594; 20050153919; 20050085486; and 20030158133; and International PCT Publication Nos. WO 00/03683 and WO 02/087541.

In some embodiments, a liposomal formulation of the invention comprises a RNAi molecule of the invention formulated or complexed with compounds and compositions described in U.S. Pat. Nos. 6,858,224; 6,534,484; 6,287,591; 6,835,395; 6,586,410; 6,858,225; 6,815,432; 6,586,001; 6,120,798; 6,977,223; 6,998,115; 5,981,501; 5,976,567; 5,705,385; and U.S. Patent Application Publication Nos. 2006/0019912; 2006/0019258; 2006/0008909; 2005/0255153; 2005/0079212; 2005/0008689; 2003/0077829, 2005/0064595, 2005/0175682, 2005/0118253; 2004/0071654; 2005/0244504; 2005/0265961 and 2003/0077829.

The present disclosure also features a method for preparing single-stranded RNAi molecule nanoparticles. A first solution containing melamine derivatives is dissolved in an organic solvent such as dimethyl sulfoxide, or dimethyl formamide to which an acid such as HCl has been added. The concentration of HCl would be about 3.3 moles of HCl for every mole of the melamine derivative. The first solution is then mixed with a second solution, which includes a nucleic acid dissolved or suspended in a polar or hydrophilic solvent (e.g., an aqueous buffer solution containing, for instance, ethylenediaminetraacetic acid (EDTA), or tris(hydroxymethyl) aminomethane (TRIS), or combinations thereof. The mixture forms a first emulsion. The mixing can be done using any standard technique such as, for example, sonication, vortexing, or in a micro fluidizer. The resultant nucleic acid particles can be purified and the organic solvent removed using size-exclusion chromatography or dialysis or both. The complexed nucleic acid nanoparticles can then be mixed with an aqueous solution containing either polyarginine or a Gln-Asn polymer, or both, in an aqueous solution. A preferred molecular weight of each polymer is about 5000 to about 15,000 Daltons. This forms a solution containing nanoparticles of nucleic acid complexed with the melamine derivative and the polyarginine and the Gln-Asn polymers. The mixing steps are carried out in a manner that minimizes shearing of the nucleic acid while producing nanoparticles on average smaller than about 200 nanometers in diameter. It is believed that the polyarginine complexes with the negative charge of the phosphate groups within the minor groove of the nucleic acid, and the polyarginine wraps around the trimeric nucleic acid complex. At either terminus of the polyarginine other moieties, such as the TAT polypeptide, mannose or galactose, can be covalently bound to the polymer to direct binding of the nucleic acid complex to specific tissues, such as to the liver when galactose is used. While not being bound to theory, it is believed that the Gln-Asn polymer complexes with the nucleic acid complex within the major groove of the nucleic acid through hydrogen bonding with the bases of the nucleic acid. The polyarginine and the Gln-Asn polymer should be present at a concentration of 2 moles per every mole of nucleic acid having 20 base pairs. The concentration should be increased proportionally for a nucleic acid having more than 20 base pairs. For example, if the nucleic acid has 25 base pairs, the concentration of the polymers should be 2.5-3 moles per mole of double-stranded nucleic acid. The resultant nanoparticles can be purified by standard means such as size exclusion chromatography followed by dialysis. The purified complexed nanoparticles can then be lyophilized using techniques well known in the art. One embodiment of the present disclosure provides nanoparticles less than 100 nanometers (nm) comprising a single-stranded RNAi molecule.

(iii) Treatment

Subjects (e.g., mammalian, human) amendable for treatment using the single-stranded RNAi molecules of the invention (optionally substituted or modified or conjugated), compositions thereof, and methods of the present disclosure include those suffering from one or more disease or condition mediated, at least in part, by an aberrant expression level of the target gene or sequence, those at risk of developing a disease caused by or associated with the aberrant levels of a target gene/sequence, or those which are amenable to treatment by replenishing or increasing the level of RNAi mediated by the corresponding ssRNAi molecule, including a hyperproliferative (e.g., cancer), angiogenic, metabolic, or inflammatory (e.g., arthritis) disease or disorder or condition.

Compositions and methods disclosed herein are useful in the treatment of a wide variety of target viruses, including retrovirus, such as human immunodeficiency virus (HIV), Hepatitis C Virus, Hepatitis B Virus, Coronavirus, as well as respiratory viruses, including human Respiratory Syncytial Virus, human Metapneumovirus, human Parainfluenza virus, Rhinovirus and Influenza virus.

In other examples, the compositions and methods of this disclosure are useful as therapeutic tools to treat or prevent symptoms of, for example, hyperproliferative disorders. Exemplary hyperproliferative disorders include neoplasms, carcinomas, sarcomas, tumors, or cancer. More exemplary hyperproliferative disorders include oral cancer, throat cancer, laryngeal cancer, esophageal cancer, pharyngeal cancer, nasopharyngeal cancer, oropharyngeal cancer, gastrointestinal tract cancer, gastrointestinal stromal tumors (GIST), small intestine cancer, colon cancer, rectal cancer, colorectal cancer, anal cancer, pancreatic cancer, breast cancer, cervical cancer, uterine cancer, vulvar cancer, vaginal cancer, urinary tract cancer, bladder cancer, kidney cancer, adrenocortical cancer, islet cell carcinoma, gallbladder cancer, stomach cancer, prostate cancer, ovarian cancer, endometrial cancer, trophoblastic tumor, testicular cancer, penial cancer, bone cancer, osteosarcoma, liver cancer, extrahepatic bile duct cancer, skin cancer, basal cell carcinoma (BCC), lung cancer, small cell lung cancer, non-small cell lung cancer (NSCLC), brain cancer, melanoma, Kaposi's sarcoma, eye cancer, head and neck cancer, squamous cell carcinoma of head and neck, tymoma, thymic carcinoma, thyroid cancer, parathyroid cancer, Hippel-Lindau syndrome, leukemia, acute myeloid leukemia, chronic myelogenous leukemia, acute lymphoblastic leukemia, hairy cell leukemia, lymphoma, non-Hodgkin's lymphoma, Burkitt's lymphoma, T-cell lymphoma, multiple myeloma, malignant pleural mesothelioma, Barrett's adenocarcinoma, Wilm's tumor, or the like. In other examples, the compositions and methods of this disclosure are useful as therapeutic tools to regulate expression of one or more target gene to treat or prevent symptoms of, for example, inflammatory disorders. Exemplary inflammatory disorders include diabetes mellitus, rheumatoid arthritis, pannus growth in inflamed synovial lining, collagen-induced arthritis, spondylarthritis, ankylosing spondylitis, multiple sclerosis, encephalomyelitis, inflammatory bowel disease, Chron's disease, psoriasis or psoriatic arthritis, myasthenia gravis, systemic lupus erythematosis, graft-versus-host disease, atherosclerosis, and allergies.

Other exemplary disorders that can be treated with single-stranded RNAi molecules, compositions and methods of the instant disclosure include metabolic disorders, cardiac disease, pulmonary disease, neovascularization, ischemic disorders, age-related macular degeneration, diabetic retinopathy, glomerulonephritis, diabetes, asthma, chronic obstructive pulmonary disease, chronic bronchitis, lymphangiogenesis, and atherosclerosis.

Within additional aspects, combination formulations and methods are provided comprising an effective amount of one or more single-stranded RNAi molecules in combination with one or more secondary or adjunctive active agents that are formulated together or administered coordinately with the single-stranded RNAi molecules of the invention to control one or more target gene-associated disease or condition as described herein. Useful adjunctive therapeutic agents in these combinatorial formulations and coordinate treatment methods include, for example, enzymatic nucleic acid molecules, allosteric nucleic acid molecules, guide, decoy, or aptamer nucleic acid molecules, antibodies such as monoclonal antibodies, small molecules and other organic or inorganic compounds including metals, salts and ions, and other drugs and active agents indicated for treating one or more target gene-associated disease or condition, including chemotherapeutic agents used to treat cancer, steroids, non-steroidal anti-inflammatory drugs (NSAIDs), or the like. Exemplary chemotherapeutic agents include alkylating agents (e.g., cisplatin, oxaliplatin, carboplatin, busulfan, nitrosoureas, nitrogen mustards, uramustine, temozolomide), antimetabolites (e.g., aminopterin, methotrexate, mercaptopurine, fluorouracil, cytarabine), taxanes (e.g., paclitaxel, docetaxel), anthracyclines (e.g., doxorubicin, daunorubicin, epirubicin, idaruicin, mitoxantrone, valrubicin), bleomycin, mytomycin, actinomycin, hydroxyurea, topoisomerase inhibitors (e.g., camptothecin, topotecan, irinotecan, etoposide, teniposide), monoclonal antibodies (e.g., alemtuzumab, bevacizumab, cetuximab, gemtuzumab, panitumumab, rituximab, tositumomab, trastuzumab), vinca alkaloids (e.g., vincristine, vinblastine, vindesine, vinorelbine), cyclophosphamide, prednisone, leucovorin, oxaliplatin.

To practice the coordinate administration methods of this disclosure, a single-stranded RNAi molecule is administered simultaneously or sequentially in a coordinated treatment protocol with one or more secondary or adjunctive therapeutic agents described herein or known in the art. The coordinate administration may be done in either order, and there may be a time period while only one or both (or all) active therapeutic agents, individually or collectively, exert their biological activities. A distinguishing aspect of all such coordinate treatment methods is that the single-stranded RNAi molecule(s) present in a composition elicits some favorable clinical response, which may or may not be in conjunction with a secondary clinical response provided by the secondary therapeutic agent. For example, the coordinate administration of a single-stranded RNAi molecule with a secondary therapeutic agent as contemplated herein can yield an enhanced (e.g., synergistic) therapeutic response beyond the therapeutic response elicited by either or both the purified single-stranded RNAi molecule and the secondary therapeutic agent alone.

A pharmaceutically effective dose is that dose required to prevent, inhibit the occurrence, or treat (alleviate a symptom to some extent, preferably all of the symptoms) a disease state. The pharmaceutically effective dose depends on the type of disease, the composition used, the route of administration, the type of subject being treated, the physical characteristics of the specific subject under consideration for treatment (e.g., age, body weight, general health, sex, diet), concurrent medication, rate of excretion, drug combination, the severity of the particular disease undergoing therapy, and other factors that those skilled in the medical arts will recognize. For example, an amount between about 0.1 mg/kg and about 140 mg/kg body weight/day of active ingredients may be administered depending on the potency of a single-stranded RNAi molecule of this disclosure (about 0.5 mg to about 7 g per patient per day). The amount of active ingredient that can be combined with the carrier materials to produce a single dosage form varies depending upon the host treated and the particular mode of administration. Dosage unit forms generally contain between from about 1 mg to about 500 mg of an active ingredient.

Nucleic acid molecules can be administered to cells or organisms by a variety of methods known to those of skill in the art, including administration of formulations that comprise a single-stranded RNAi molecule, or formulations that further comprise one or more additional components, such as a pharmaceutically acceptable carrier, diluent, excipient, adjuvant, emulsifier, buffer, stabilizer, preservative, or the like. In certain embodiments, a single-stranded RNAi molecule of the invention, and/or the polypeptide can be encapsulated in liposomes, administered by iontophoresis, or incorporated into other vehicles, such as hydrogels, cyclodextrins, biodegradable nanocapsules, bioadhesive microspheres, or proteinaceous vectors (see, e.g., PCT Publication No. WO 00/53722). Alternatively, a nucleic acid/peptide/vehicle combination can be locally delivered by direct injection or by use of an infusion pump. Direct injection of the nucleic acid molecules of this disclosure, whether subcutaneous, intramuscular, or intradermal, can take place using standard needle and syringe methodologies, or by needle-free technologies, such as those described in Conroy et al, (1999, Clin. Cancer Res. 5:2330) and PCT Publication No. WO 99/31262.

The formulations of the present disclosure, having an amount of a single-stranded RNAi molecule sufficient to treat or prevent a disorder associated with target gene expression are, for example, suitable for topical (e.g., creams, ointments, skin patches, eye drops, ear drops) application or administration. Other routes of administration include oral, parenteral, sublingual, bladder washout, vaginal, rectal, enteric, suppository, nasal, and inhalation. The term “parenteral,” as used herein, includes subcutaneous, intravenous, intramuscular, intraarterial, intraabdominal, intraperitoneal, intraarticular, intraocular or retrobulbar, intraaural, intrathecal, intracavitary, intracelial, intraspinal, intrapulmonary or transpulmonary, intrasynovial, and intraurethral injection or infusion techniques. The compositions of the present disclosure may also be formulated and used as a tablet, capsule or elixir for oral administration, suppository for rectal administration, sterile solution, or suspension for injectable administration, either with or without other compounds known in the art. For administration to non-human animals, the composition can also be added to the animal feed or drinking water. It can be convenient to formulate the animal feed and drinking water compositions so that the animal takes in a therapeutically appropriate quantity of the composition along with its diet. It can also be convenient to present the composition as a premix for addition to the feed or drinking water.

Further methods for delivery of nucleic acid molecules, such as single-stranded RNAi molecules of this invention, have been described in, for example, Boado et al., 1998, J. Pharm. Sci 87:1308; Tyler et al., 1999, FEBS Lett. 421:2m; Pardridge et al., 1995, Proc. Nat'l Acad. Sci. USA 92:5592; Boado, 1995, Adv. Drug Delivery Rev. 15:73; Aldrian-Herrada et al. 1998, Nucleic Acids Res. 26:4910; Tyler et al., 1999, Proc. Nat'l Acad. Sci. USA 96:7053; Akhtar et al., 1992, Trends Cell Bio. 2:139; “Delivery Strategies for Guide Oligonucleotide Therapeutics,” ed. Akhtar, 1995, Maurer et al., 1999 Mol. Membr. Biol. 16:129; Lee et al., 2000, ACS Symp. Ser. 752:184. In addition to in vivo and therapeutic applications, a skilled person in the art will appreciate that the single-stranded RNAi molecules of the present disclosure are useful in a wide variety of in vitro applications, such as in scientific and commercial research (e.g., elucidation of physiological pathways, drug discovery and development), and medical and veterinary diagnostics.

All U.S. patents, U.S. patent publications, U.S. patent applications, foreign patents, foreign patent applications, non-patent publications, figures, and websites referred to in this specification are expressly incorporated herein by reference, in their entirety.

Table 1 lists certain endogenous human miRNA sequences, wherein the seed sequences, confirmed or projected, are capitalized. All miRNA sequences in Table 1 are shown in 5′ to 3′ orientation. Other miRNA sequences of the present invention may be found in the miRBase database, the content of which is incorporated by reference herein.

TABLE 1 SEQ ID miRNA name miRBase number Sequence NO hsa-let-7a MIMAT0000062 UGAGGUAGuagguuguauaguu 1 hsa-1et-7a* MIMAT0004481 CUAUACAAucuacugucuuuc 2 hsa-1et-7a-2* MIMAT0010195 CUGUACAGccuccuagcuuucc 3 hsa-let-7b MIMAT0000063 UGAGGUAGuagguugugugguu 4 hsa-1et-7b* MIMAT0004482 CUAUACAAccuacugccuuccc 5 hsa-let-7c MIMAT0000064 UGAGGUAGuagguuguaugguu 6 hsa-1et-7c* MIMAT0004483 UAGAGUUAcacccugggaguua 7 hsa-let-7d MIMAT0000065 AGAGGUAGuagguugcauaguu 8 hsa-1et-7d* MIMAT0004484 CUAUACGAccugcugccuuucu 9 hsa-let-7e MIMAT0000066 UGAGGUAGgagguuguauaguu 10 hsa-1et-7e* MIMAT0004485 CUAUACGGccuccuagcuuucc 11 hsa-let-7f MIMAT0000067 UGAGGUAGuagauuguauaguu 12 hsa-let-7f-1* MIMAT0004486 CUAUACAAucuauugccuuccc 13 hsa-1et-7f-2* MIMAT0004487 CUAUACAGucuacugucuuucc 14 hsa-miR-15a MIMAT0000068 UAGCAGCAcauaaugguuugug 15 hsa-miR-15a* MIMAT0004488 CAGGCCAUauugugcugccuca 16 hsa-miR-16 MIMAT0000069 UAGCAGCAcguaaauauuggcg 17 hsa-miR-16-1* MIMAT0004489 CCAGUAUUaacugugcugcuga 18 hsa-miR-17 MIMAT0000070 CAAAGUGCuuacagugcagguag 19 hsa-miR-17* MIMAT0000071 ACUGCAGUgaaggcacuuguag 20 hsa-miR-18a MIMAT0000072 UAAGGUGCaucuagugcagauag 21 hsa-miR-18a* MIMAT0002891 ACUGCCCUaagugcuccuucugg 22 hsa-miR-19a* MIMAT0004490 AGUUUUGCauaguugcacuaca 23 hsa-miR-19a MIMAT0000073 UGUGCAAAucuaugcaaaacuga 24 hsa-miR-19b-1* MIMAT0004491 AGUUUUGCagguuugcauccagc 25 hsa-miR-19b MIMAT0000074 UGUGCAAAuccaugcaaaacuga 26 hsa-miR-19b-2* MIMAT0004492 AGUUUUGCagguuugcauuuca 27 hsa-miR-20a MIMAT0000075 UAAAGUGCuuauagugcagguag 28 hsa-miR-20a* MIMAT0004493 ACUGCAUUaugagcacuuaaag 29 hsa-miR-21 MIMAT0000076 UAGCUUAUcagacugauguuga 30 hsa-miR-21* MIMAT0004494 CAACACCAgucgaugggcugu 31 hsa-miR-22* MIMAT0004495 AGUUCUUCaguggcaagcuuua 32 hsa-miR-22 MIMAT0000077 AAGCUGCCaguugaagaacugu 33 hsa-miR-23a* MIMAT0004496 GGGGUUCCuggggaugggauuu 34 hsa-miR-23a MIMAT0000078 AUCACAUUgccagggauuucc 35 hsa-miR-24-1* MIMAT0000079 UGCCUACUgagcugauaucagu 36 hsa-miR-24 MIMAT0000080 UGGCUCAGuucagcaggaacag 37 hsa-miR-24-2* MIMAT0004497 UGCCUACUgagcugaaacacag 38 hsa-miR-25* MIMAT0004498 AGGCGGAGacuugggcaauug 39 hsa-miR-25 MIMAT0000081 CAUUGCACuugucucggucuga 40 hsa-miR-26a MIMAT0000082 UUCAAGUAauccaggauaggcu 41 hsa-miR-26a-1* MIMAT0004499 CCUAUUCUugguuacuugcacg 42 hsa-miR-26b MIMAT0000083 UUCAAGUAauucaggauaggu 43 hsa-miR-26b* MIMAT0004500 CCUGUUCUccauuacuuggcuc 44 hsa-miR-27a* MIMAT0004501 AGGGCUUAgcugcuugugagca 45 hsa-miR-27a MIMAT0000084 UUCACAGUggcuaaguuccgc 46 hsa-miR-28-5p MIMAT0000085 AAGGAGCUcacagucuauugag 47 hsa-miR-28-3p MIMAT0004502 CACUAGAUugugagcuccugga 48 hsa-miR-29a* MIMAT0004503 ACUGAUUUcuuuugguguucag 49 hsa-miR-29a MIMAT0000086 UAGCACCAucugaaaucgguua 50 hsa-miR-30a MIMAT0000087 UGUAAACAuccucgacuggaag 51 hsa-miR-30a* MIMAT0000088 CUUUCAGUcggauguuugcagc 52 hsa-miR-31 MIMAT0000089 AGGCAAGAugcuggcauagcu 53 hsa-miR-31* MIMAT0004504 UGCUAUGCcaacauauugccau 54 hsa-miR-32 MIMAT0000090 UAUUGCACauuacuaaguugca 55 hsa-miR-32* MIMAT0004505 CAAUUUAGugugugugauauuu 56 hsa-miR-33a MIMAT0000091 GUGCAUUGuaguugcauugca 57 hsa-miR-33a* MIMAT0004506 CAAUGUUUccacagugcaucac 58 hsa-miR-92a-1* MIMAT0004507 AGGUUGGGaucgguugcaaugcu 59 hsa-miR-92a MIMAT0000092 UAUUGCACuugucccggccugu 60 hsa-miR-92a-2* MIMAT0004508 GGGUGGGGauuuguugcauuac 61 hsa-miR-93 MIMAT0000093 CAAAGUGCuguucgugcagguag 62 hsa-miR-93* MIMAT0004509 ACUGCUGAgcuagcacuucccg 63 hsa-miR-95 MIMAT0000094 UUCAACGGguauuuauugagca 64 hsa-miR-96 MIMAT0000095 UUUGGCACuagcacauuuuugcu 65 hsa-miR-96* MIMAT0004510 AAUCAUGUgcagugccaauaug 66 hsa-miR-98 MIMAT0000096 UGAGGUAGuaaguuguauuguu 67 hsa-miR-99a MIMAT0000097 AACCCGUAgauccgaucuugug 68 hsa-miR-99a* MIMAT0004511 CAAGCUCGcuucuaugggucug 69 hsa-miR-100 MIMAT0000098 AACCCGUAgauccgaacuugug 70 hsa-miR-100* MIMAT0004512 CAAGCUUGuaucuauagguaug 71 hsa-miR-101* MIMAT0004513 CAGUUAUCacagugcugaugcu 72 hsa-miR-101 MIMAT0000099 UACAGUACugugauaacugaa 73 hsa-miR-29b-1* MIMAT0004514 GCUGGUUUcauauggugguuuaga 74 hsa-miR-29b MIMAT0000100 UAGCACCAuuugaaaucaguguu 75 hsa-miR-29b-2* MIMAT0004515 CUGGUUUCacaugguggcuuag 76 hsa-miR-103-2* MIMAT0009196 AGCUUCUUuacagugcugccuug 77 hsa-miR-103 MIMAT0000101 AGCAGCAUuguacagggcuauga 78 hsa-miR-105 MIMAT0000102 UCAAAUGCucagacuccuguggu 79 hsa-miR-105* MIMAT0004516 ACGGAUGUuugagcaugugcua 80 hsa-miR-106a MIMAT0000103 AAAAGUGCuuacagugcagguag 81 hsa-miR-106a* MIMAT0004517 CUGCAAUGuaagcacuucuuac 82 hsa-miR-107 MIMAT0000104 AGCAGCAUuguacagggcuauca 83 hsa-miR-16-2* MIMAT0004518 CCAAUAUUacugugcugcuuua 84 hsa-miR-192 MIMAT0000222 CUGACCUAugaauugacagcc 85 hsa-miR-192* MIMAT0004543 CUGCCAAUuccauaggucacag 86 hsa-miR-196a MIMAT0000226 UAGGUAGUuucauguuguuggg 87 hsa-miR-197 MIMAT0000227 UUCACCACcuucuccacccagc 88 hsa-miR-198 MIMAT0000228 GGUCCAGAggggagauagguuc 89 hsa-miR-199a-5p MIMAT0000231 CCCAGUGUucagacuaccuguuc 90 hsa-miR-199a-3p MIMAT0000232 ACAGUAGUcugcacauugguua 91 hsa-miR-208a MIMAT0000241 AUAAGACGagcaaaaagcuugu 92 hsa-miR-129-5p MIMAT0000242 CUUUUUGCggucugggcuugc 93 hsa-miR-129* MIMAT0004548 AAGCCCUUaccccaaaaaguau 94 hsa-miR-148a* MIMAT0004549 AAAGUUCUgagacacuccgacu 95 hsa-miR-148a MIMAT0000243 UCAGUGCAcuacagaacuuugu 96 hsa-miR-30c MIMAT0000244 UGUAAACAuccuacacucucagc 97 hsa-miR-30c-2* MIMAT0004550 CUGGGAGAaggcuguuuacucu 98 hsa-miR-30d MIMAT0000245 UGUAAACAuccccgacuggaag 99 hsa-miR-30d* MIMAT0004551 CUUUCAGUcagauguuugcugc 100 hsa-miR-139-5p MIMAT0000250 UCUACAGUgcacgugucuccag 101 hsa-miR-139-3p MIMAT0004552 GGAGACGCggcccuguuggagu 102 hsa-miR-147 MIMAT0000251 GUGUGUGGaaaugcuucugc 103 hsa-miR-7 MIMAT0000252 UGGAAGACuagugauuuuguugu 104 hsa-miR-7-1* MIMAT0004553 CAACAAAUcacagucugccaua 105 hsa-miR-7-2* MIMAT0004554 CAACAAAUcccagucuaccuaa 106 hsa-miR-10a MIMAT0000253 UACCCUGUagauccgaauuugug 107 hsa-miR-10a* MIMAT0004555 CAAAUUCGuaucuaggggaaua 108 hsa-miR-10b MIMAT0000254 UACCCUGUagaaccgaauuugug 109 hsa-miR-10b* MIMAT0004556 ACAGAUUCgauucuaggggaau 110 hsa-miR-34a MIMAT0000255 UGGCAGUGucuuagcugguugu 111 hsa-miR-34a* MIMAT0004557 CAAUCAGCaaguauacugcccu 112 hsa-miR-181a MIMAT0000256 AACAUUCAacgcugucggugagu 113 hsa-miR-181a2* MIMAT0004558 ACCACUGAccguugacuguacc 114 hsa-miR-181b MIMAT0000257 AACAUUCAuugcugucggugggu 115 hsa-miR-181c MIMAT0000258 AACAUUCAaccugucggugagu 116 hsa-miR-181c* MIMAT0004559 AACCAUCGaccguugaguggac 117 hsa-miR-182 MIMAT0000259 UUUGGCAAugguagaacucacacu 118 hsa-miR-182* MIMAT0000260 UGGUUCUAgacuugccaacua 119 hsa-miR-183 MIMAT0000261 UAUGGCACugguagaauucacu 120 hsa-miR-183* MIMAT0004560 GUGAAUUAccgaagggccauaa 121 hsa-miR-187* MIMAT0004561 GGCUACAAcacaggacccgggc 122 hsa-miR-187 MIMAT0000262 UCGUGUCUuguguugcagccgg 123 hsa-miR-196a* MIMAT0004562 CGGCAACAagaaacugccugag 124 hsa-miR-199b-5p MIMAT0000263 CCCAGUGUuuagacuaucuguuc 125 hsa-miR-199b-3p MIMAT0004563 ACAGUAGUcugcacauugguua 91 hsa-miR-203 MIMAT0000264 GUGAAAUGuuuaggaccacuag 126 hsa-miR-204 MIMAT0000265 UUCCCUUUgucauccuaugccu 127 hsa-miR-205 MIMAT0000266 UCCUUCAUuccaccggagucug 128 hsa-miR-205* MIMAT0009197 GAUUUCAGuggagugaaguuc 129 hsa-miR-210 MIMAT0000267 CUGUGCGUgugacagcggcuga 130 hsa-miR-211 MIMAT0000268 UUCCCUUUgucauccuucgccu 131 hsa-miR-212 MIMAT0000269 UAACAGUCuccagucacggcc 132 hsa-miR-181a* MIMAT0000270 ACCAUCGAccguugauuguacc 133 hsa-miR-214* MIMAT0004564 UGCCUGUCuacacuugcugugc 134 hsa-miR-214 MIMAT0000271 ACAGCAGGcacagacaggcagu 135 hsa-miR-215 MIMAT0000272 AUGACCUAugaauugacagac 136 hsa-miR-216a MIMAT0000273 UAAUCUCAgcuggcaacuguga 137 hsa-miR-217 MIMAT0000274 UACUGCAUcaggaacugauugga 138 hsa-miR-218 MIMAT0000275 UUGUGCUUgaucuaaccaugu 139 hsa-miR-218-1* MIMAT0004565 AUGGUUCCgucaagcaccaugg 140 hsa-miR-218-2* MIMAT0004566 CAUGGUUCugucaagcaccgcg 141 hsa-miR-219-5p MIMAT0000276 UGAUUGUCcaaacgcaauucu 142 hsa-miR-219-1-3p MIMAT0004567 AGAGUUGAgucuggacgucccg 143 hsa-miR-220a MIMAT0000277 CCACACCGuaucugacacuuu 144 hsa-miR-221* MIMAT0004568 ACCUGGCAuacaauguagauuu 145 hsa-miR-221 MIMAT0000278 AGCUACAUugucugcuggguuuc 146 hsa-miR-222* MIMAT0004569 CUCAGUAGccaguguagauccu 147 hsa-miR-222 MIMAT0000279 AGCUACAUcuggcuacugggu 148 hsa-miR-223* MIMAT0004570 CGUGUAUUugacaagcugaguu 149 hsa-miR-223 MIMAT0000280 UGUCAGUUugucaaauacccca 150 hsa-miR-224 MIMAT0000281 CAAGUCACuagugguuccguu 151 hsa-miR-224* MIMAT0009198 AAAAUGGUgcccuagugacuaca 152 hsa-miR-200b* MIMAT0004571 CAUCUUACugggcagcauugga 153 hsa-miR-200b MIMAT0000318 UAAUACUGccugguaaugauga 154 hsa-let-7g MIMAT0000414 UGAGGUAGuaguuuguacaguu 155 hsa-1et-7g* MIMAT0004584 CUGUACAGgccacugccuugc 156 hsa-let-7i MIMAT0000415 UGAGGUAGuaguuugugcuguu 157 hsa-1et-7i* MIMAT0004585 CUGCGCAAgcuacugccuugcu 158 hsa-miR-1 MIMAT0000416 UGGAAUGUaaagaaguauguau 159 hsa-miR-15b MIMAT0000417 UAGCAGCAcaucaugguuuaca 160 hsa-miR-15b* MIMAT0004586 CGAAUCAUuauuugcugcucua 161 hsa-miR-23b* MIMAT0004587 UGGGUUCCuggcaugcugauuu 162 hsa-miR-23b MIMAT0000418 AUCACAUUgccagggauuacc 163 hsa-miR-27b* MIMAT0004588 AGAGCUUAgcugauuggugaac 164 hsa-miR-27b MIMAT0000419 UUCACAGUggcuaaguucugc 165 hsa-miR-30b MIMAT0000420 UGUAAACAuccuacacucagcu 166 hsa-miR-30b* MIMAT0004589 CUGGGAGGuggauguuuacuuc 167 hsa-miR-122 MIMAT0000421 UGGAGUGUgacaaugguguuug 168 hsa-miR-122* MIMAT0004590 AACGCCAUuaucacacuaaaua 169 hsa-miR-124* MIMAT0004591 CGUGUUCAcagcggaccuugau 170 hsa-miR-124 MIMAT0000422 UAAGGCACgcggugaaugcc 171 hsa-miR-125b MIMAT0000423 UCCCUGAGacccuaacuuguga 172 hsa-miR-125b-1* MIMAT0004592 ACGGGUUAggcucuugggagcu 173 hsa-miR-128 MIMAT0000424 UCACAGUGaaccggucucuuu 174 hsa-miR-130a* MIMAT0004593 UUCACAUUgugcuacugucugc 175 hsa-miR-130a MIMAT0000425 CAGUGCAAuguuaaaagggcau 176 hsa-miR-132* MIMAT0004594 ACCGUGGCuuucgauuguuacu 177 hsa-miR-132 MIMAT0000426 UAACAGUCuacagccauggucg 178 hsa-miR-133a MIMAT0000427 UUUGGUCCccuucaaccagcug 179 hsa-miR-135a MIMAT0000428 UAUGGCUUuuuauuccuauguga 180 hsa-miR-135a* MIMAT0004595 UAUAGGGAuuggagccguggcg 181 hsa-miR-137 MIMAT0000429 UUAUUGCUuaagaauacgcguag 182 hsa-miR-138 MIMAT0000430 AGCUGGUGuugugaaucaggccg 183 hsa-miR-138-2* MIMAT0004596 GCUAUUUCacgacaccaggguu 184 hsa-miR-140-5p MIMAT0000431 CAGUGGUUuuacccuaugguag 185 hsa-miR-140-3p MIMAT0004597 UACCACAGgguagaaccacgg 186 hsa-miR-141* MIMAT0004598 CAUCUUCCaguacaguguugga 187 hsa-miR-141 MIMAT0000432 UAACACUGucugguaaagaugg 188 hsa-miR-142-5p MIMAT0000433 CAUAAAGUagaaagcacuacu 189 hsa-miR-142-3p MIMAT0000434 UGUAGUGUuuccuacuuuaugga 190 hsa-miR-143* MIMAT0004599 GGUGCAGUgcugcaucucuggu 191 hsa-miR-143 MIMAT0000435 UGAGAUGAagcacuguagcuc 192 hsa-miR-144* MIMAT0004600 GGAUAUCAucauauacuguaag 193 hsa-miR-144 MIMAT0000436 UACAGUAUagaugauguacu 194 hsa-miR-145 MIMAT0000437 GUCCAGUUuucccaggaaucccu 195 hsa-miR-145* MIMAT0004601 GGAUUCCUggaaauacuguucu 196 hsa-miR-152 MIMAT0000438 UCAGUGCAugacagaacuugg 197 hsa-miR-153 MIMAT0000439 UUGCAUAGucacaaaagugauc 198 hsa-miR-191 MIMAT0000440 CAACGGAAucccaaaagcagcug 199 hsa-miR-191* MIMAT0001618 GCUGCGCUuggauuucgucccc 200 hsa-miR-9 MIMAT0000441 UCUUUGGUuaucuagcuguauga 201 hsa-miR-9* MIMAT0000442 AUAAAGCUagauaaccgaaagu 202 hsa-miR-125a-5p MIMAT0000443 UCCCUGAGacccuuuaaccuguga 203 hsa-miR-125a-3p MIMAT0004602 ACAGGUGAgguucuugggagcc 204 hsa-miR-125b-2* MIMAT0004603 UCACAAGUcaggcucuugggac 205 hsa-miR-126* MIMAT0000444 CAUUAUUAcuuuugguacgcg 206 hsa-miR-126 MIMAT0000445 UCGUACCGugaguaauaaugcg 207 hsa-miR-127-5p MIMAT0004604 CUGAAGCUcagagggcucugau 208 hsa-miR-127-3p MIMAT0000446 UCGGAUCCgucugagcuuggcu 209 hsa-miR-129-3p MIMAT0004605 AAGCCCUUaccccaaaaagcau 210 hsa-miR-134 MIMAT0000447 UGUGACUGguugaccagagggg 211 hsa-miR-136 MIMAT0000448 ACUCCAUUuguuuugaugaugga 212 hsa-miR-136* MIMAT0004606 CAUCAUCGucucaaaugagucu 213 hsa-miR-138-1* MIMAT0004607 GCUACUUCacaacaccagggcc 214 hsa-miR-146a MIMAT0000449 UGAGAACUgaauuccauggguu 215 hsa-miR-146a* MIMAT0004608 CCUCUGAAauucaguucuucag 216 hsa-miR-149 MIMAT0000450 UCUGGCUCcgugucuucacuccc 217 hsa-miR-149* MIMAT0004609 AGGGAGGGacgggggcugugc 218 hsa-miR-150 MIMAT0000451 UCUCCCAAcccuuguaccagug 219 hsa-miR-150* MIMAT0004610 CUGGUACAggccugggggacag 220 hsa-miR-154 MIMAT0000452 UAGGUUAUccguguugccuucg 221 hsa-miR-154* MIMAT0000453 AAUCAUACacgguugaccuauu 222 hsa-miR-184 MIMAT0000454 UGGACGGAgaacugauaagggu 223 hsa-miR-185 MIMAT0000455 UGGAGAGAaaggcaguuccuga 224 hsa-miR-185* MIMAT0004611 AGGGGCUGgcuuuccucugguc 225 hsa-miR-186 MIMAT0000456 CAAAGAAUucuccuuuugggcu 226 hsa-miR-186* MIMAT0004612 GCCCAAAGgugaauuuuuuggg 227 hsa-miR-188-5p MIMAT0000457 CAUCCCUUgcaugguggaggg 228 hsa-miR-188-3p MIMAT0004613 CUCCCACAugcaggguuugca 229 hsa-miR-190 MIMAT0000458 UGAUAUGUuugauauauuaggu 230 hsa-miR-193a-5p MIMAT0004614 UGGGUCUUugcgggcgagauga 231 hsa-miR-193a-3p MIMAT0000459 AACUGGCCuacaaagucccagu 232 hsa-miR-194 MIMAT0000460 UGUAACAGcaacuccaugugga 233 hsa-miR-195 MIMAT0000461 UAGCAGCAcagaaauauuggc 234 hsa-miR-195* MIMAT0004615 CCAAUAUUggcugugcugcucc 235 hsa-miR-206 MIMAT0000462 UGGAAUGUaaggaagugugugg 236 hsa-miR-320a MIMAT0000510 AAAAGCUGgguugagagggcga 237 hsa-miR-200c* MIMAT0004657 CGUCUUACccagcaguguuugg 238 hsa-miR-200c MIMAT0000617 UAAUACUGccggguaaugaugga 239 hsa-miR-155 MIMAT0000646 UUAAUGCUaaucgugauaggggu 240 hsa-miR-155* MIMAT0004658 CUCCUACAuauuagcauuaaca 241 hsa-miR-194* MIMAT0004671 CCAGUGGGgcugcuguuaucug 242 hsa-miR-106b MIMAT0000680 UAAAGUGCugacagugcagau 243 hsa-miR-106b* MIMAT0004672 CCGCACUGuggguacuugcugc 244 hsa-miR-29c* MIMAT0004673 UGACCGAUuucuccugguguuc 245 hsa-miR-29c MIMAT0000681 UAGCACCAuuugaaaucgguua 246 hsa-miR-30c-1* MIMAT0004674 CUGGGAGAggguuguuuacucc 247 hsa-miR-200a* MIMAT0001620 CAUCUUACcggacagugcugga 248 hsa-miR-200a MIMAT0000682 UAACACUGucugguaacgaugu 249 hsa-miR-302a* MIMAT0000683 ACUUAAACguggauguacuugcu 250 hsa-miR-302a MIMAT0000684 UAAGUGCUuccauguuuugguga 251 hsa-miR-219-2-3p MIMAT0004675 AGAAUUGUggcuggacaucugu 252 hsa-miR-34b* MIMAT0000685 UAGGCAGUgucauuagcugauug 253 hsa-miR-34b MIMAT0004676 CAAUCACUaacuccacugccau 254 hsa-miR-34c-5p MIMAT0000686 AGGCAGUGuaguuagcugauugc 255 hsa-miR-34c-3p MIMAT0004677 AAUCACUAaccacacggccagg 256 hsa-miR-299-5p MIMAT0002890 UGGUUUACcgucccacauacau 257 hsa-miR-299-3p MIMAT0000687 UAUGUGGGaugguaaaccgcuu 258 hsa-miR-301a MIMAT0000688 CAGUGCAAuaguauugucaaagc 259 hsa-miR-99b MIMAT0000689 CACCCGUAgaaccgaccuugcg 260 hsa-miR-99b* MIMAT0004678 CAAGCUCGugucuguggguccg 261 hsa-miR-296-5p MIMAT0000690 AGGGCCCCcccucaauccugu 262 hsa-miR-296-3p MIMAT0004679 GAGGGUUGgguggaggcucucc 263 hsa-miR-130b* MIMAT0004680 ACUCUUUCccuguugcacuac 264 hsa-miR-130b MIMAT0000691 CAGUGCAAugaugaaagggcau 265 hsa-miR-30e MIMAT0000692 UGUAAACAuccuugacuggaag 266 hsa-miR-30e* MIMAT0000693 CUUUCAGUcggauguuuacagc 267 hsa-miR-26a-2* MIMAT0004681 CCUAUUCUugauuacuuguuuc 268 hsa-miR-361-5p MIMAT0000703 UUAUCAGAaucuccagggguac 269 hsa-miR-361-3p MIMAT0004682 UCCCCCAGgugugauucugauuu 270 hsa-miR-362-5p MIMAT0000705 AAUCCUUGgaaccuaggugugagu 271 hsa-miR-362-3p MIMAT0004683 AACACACCuauucaaggauuca 272 hsa-miR-363* MIMAT0003385 CGGGUGGAucacgaugcaauuu 273 hsa-miR-363 MIMAT0000707 AAUUGCACgguauccaucugua 274 hsa-miR-365 MIMAT0000710 UAAUGCCCcuaaaaauccuuau 275 hsa-miR-365* MIMAT0009199 AGGGACUUucaggggcagcugu 276 hsa-miR-302b* MIMAT0000714 ACUUUAACauggaagugcuuuc 277 hsa-miR-302b MIMAT0000715 UAAGUGCUuccauguuuuaguag 278 hsa-miR-302c* MIMAT0000716 UUUAACAUggggguaccugcug 279 hsa-miR-302c MIMAT0000717 UAAGUGCUuccauguuucagugg 280 hsa-miR-302d* MIMAT0004685 ACUUUAACauggaggcacuugc 281 hsa-miR-302d MIMAT0000718 UAAGUGCUuccauguuugagugu 282 hsa-miR-367* MIMAT0004686 ACUGUUGCuaauaugcaacucu 283 hsa-miR-367 MIMAT0000719 AAUUGCACuuuagcaaugguga 284 hsa-miR-376c MIMAT0000720 AACAUAGAggaaauuccacgu 285 hsa-miR-369-5p MIMAT0001621 AGAUCGACcguguuauauucgc 286 hsa-miR-369-3p MIMAT0000721 AAUAAUACaugguugaucuuu 287 hsa-miR-370 MIMAT0000722 GCCUGCUGggguggaaccuggu 288 hsa-miR-371-5p MIMAT0004687 ACUCAAACugugggggcacu 289 hsa-miR-371-3p MIMAT0000723 AAGUGCCGccaucuuuugagugu 290 hsa-miR-372 MIMAT0000724 AAAGUGCUgcgacauuugagcgu 291 hsa-miR-373* MIMAT0000725 ACUCAAAAugggggcgcuuucc 292 hsa-miR-373 MIMAT0000726 GAAGUGCUucgauuuuggggugu 293 hsa-miR-374a MIMAT0000727 UUAUAAUAcaaccugauaagug 294 hsa-miR-374a* MIMAT0004688 CUUAUCAGauuguauuguaauu 295 hsa-miR-375 MIMAT0000728 UUUGUUCGuucggcucgcguga 296 hsa-miR-376a* MIMAT0003386 GUAGAUUCuccuucuaugagua 297 hsa-miR-376a MIMAT0000729 AUCAUAGAggaaaauccacgu 298 hsa-miR-377* MIMAT0004689 AGAGGUUGcccuuggugaauuc 299 hsa-miR-377 MIMAT0000730 AUCACACAaaggcaacuuuugu 300 hsa-miR-378* MIMAT0000731 CUCCUGACuccagguccugugu 301 hsa-miR-378 MIMAT0000732 ACUGGACUuggagucagaagg 302 hsa-miR-379 MIMAT0000733 UGGUAGACuauggaacguagg 303 hsa-miR-379* MIMAT0004690 UAUGUAACaugguccacuaacu 304 hsa-miR-380* MIMAT0000734 UGGUUGACcauagaacaugcgc 305 hsa-miR-380 MIMAT0000735 UAUGUAAUaugguccacaucuu 306 hsa-miR-381 MIMAT0000736 UAUACAAGggcaagcucucugu 307 hsa-miR-382 MIMAT0000737 GAAGUUGUucgugguggauucg 308 hsa-miR-383 MIMAT0000738 AGAUCAGAaggugauuguggcu 309 hsa-miR-340 MIMAT0004692 UUAUAAAGcaaugagacugauu 310 hsa-miR-340* MIMAT0000750 UCCGUCUCaguuacuuuauagc 311 hsa-miR-330-5p MIMAT0004693 UCUCUGGGccugugucuuaggc 312 hsa-miR-330-3p MIMAT0000751 GCAAAGCAcacggccugcagaga 313 hsa-miR-328 MIMAT0000752 CUGGCCCUcucugcccuuccgu 314 hsa-miR-342-5p MIMAT0004694 AGGGGUGCuaucugugauuga 315 hsa-miR-342-3p MIMAT0000753 UCUCACACagaaaucgcacccgu 316 hsa-miR-337-5p MIMAT0004695 GAACGGCUucauacaggaguu 317 hsa-miR-337-3p MIMAT0000754 CUCCUAUAugaugccuuucuuc 318 hsa-miR-323-5p MIMAT0004696 AGGUGGUCcguggcgcguucgc 319 hsa-miR-323-3p MIMAT0000755 CACAUUACacggucgaccucu 320 hsa-miR-326 MIMAT0000756 CCUCUGGGcccuuccuccag 321 hsa-miR-151-5p MIMAT0004697 UCGAGGAGcucacagucuagu 322 hsa-miR-151-3p MIMAT0000757 CUAGACUGaagcuccuugagg 323 hsa-miR-135b MIMAT0000758 UAUGGCUUuucauuccuauguga 324 hsa-miR-135b* MIMAT0004698 AUGUAGGGcuaaaagccauggg 325 hsa-miR-148b* MIMAT0004699 AAGUUCUGuuauacacucaggc 326 hsa-miR-148b MIMAT0000759 UCAGUGCAucacagaacuuugu 327 hsa-miR-331-5p MIMAT0004700 CUAGGUAUggucccagggaucc 328 hsa-miR-331-3p MIMAT0000760 GCCCCUGGgccuauccuagaa 329 hsa-miR-324-5p MIMAT0000761 CGCAUCCCcuagggcauuggugu 330 hsa-miR-324-3p MIMAT0000762 ACUGCCCCaggugcugcugg 331 hsa-miR-338-5p MIMAT0004701 AACAAUAUccuggugcugagug 332 hsa-miR-338-3p MIMAT0000763 UCCAGCAUcagugauuuuguug 333 hsa-miR-339-5p MIMAT0000764 UCCCUGUCcuccaggagcucacg 334 hsa-miR-339-3p MIMAT0004702 UGAGCGCCucgacgacagagccg 335 hsa-miR-335 MIMAT0000765 UCAAGAGCaauaacgaaaaaugu 336 hsa-miR-335* MIMAT0004703 UUUUUCAUuauugcuccugacc 337 hsa-miR-133b MIMAT0000770 UUUGGUCCccuucaaccagcua 338 hsa-miR-325 MIMAT0000771 CCUAGUAGguguccaguaagugu 339 hsa-miR-345 MIMAT0000772 GCUGACUCcuaguccagggcuc 340 hsa-miR-346 MIMAT0000773 UGUCUGCCcgcaugccugccucu 341 hsa-miR-384 MIMAT0001075 AUUCCUAGaaauuguucaua 342 hsa-miR-196b MIMAT0001080 UAGGUAGUuuccuguuguuggg 343 hsa-miR-196b* MIMAT0009201 UCGACAGCacgacacugccuuc 344 hsa-miR-422a MIMAT0001339 ACUGGACUuagggucagaaggc 345 hsa-miR-423-5p MIMAT0004748 UGAGGGGCagagagcgagacuuu 346 hsa-miR-423-3p MIMAT0001340 AGCUCGGUcugaggccccucagu 347 hsa-miR-424 MIMAT0001341 CAGCAGCAauucauguuuugaa 348 hsa-miR-424* MIMAT0004749 CAAAACGUgaggcgcugcuau 349 hsa-miR-425 MIMAT0003393 AAUGACACgaucacucccguuga 350 hsa-miR-425* MIMAT0001343 AUCGGGAAugucguguccgccc 351 hsa-miR-18b MIMAT0001412 UAAGGUGCaucuagugcaguuag 352 hsa-miR-18b* MIMAT0004751 UGCCCUAAaugccccuucuggc 353 hsa-miR-20b MIMAT0001413 CAAAGUGCucauagugcagguag 354 hsa-miR-20b* MIMAT0004752 ACUGUAGUaugggcacuuccag 355 hsa-miR-448 MIMAT0001532 UUGCAUAUguaggaugucccau 356 hsa-miR-429 MIMAT0001536 UAAUACUGucugguaaaaccgu 357 hsa-miR-449a MIMAT0001541 UGGCAGUGuauuguuagcuggu 358 hsa-miR-450a MIMAT0001545 UUUUGCGAuguguuccuaauau 359 hsa-miR-431 MIMAT0001625 UGUCUUGCaggccgucaugca 360 hsa-miR-431* MIMAT0004757 CAGGUCGUcuugcagggcuucu 361 hsa-miR-433 MIMAT0001627 AUCAUGAUgggcuccucggugu 362 hsa-miR-329 MIMAT0001629 AACACACCugguuaaccucuuu 363 hsa-miR-451 MIMAT0001631 AAACCGUUaccauuacugaguu 364 hsa-miR-452 MIMAT0001635 AACUGUUUgcagaggaaacuga 365 hsa-miR-452* MIMAT0001636 CUCAUCUGcaaagaaguaagug 366 hsa-miR-409-5p MIMAT0001638 AGGUUACCcgagcaacuuugcau 367 hsa-miR-409-3p MIMAT0001639 GAAUGUUGcucggugaaccccu 368 hsa-miR-412 MIMAT0002170 ACUUCACCugguccacuagccgu 369 hsa-miR-410 MIMAT0002171 AAUAUAACacagauggccugu 370 hsa-miR-376b MIMAT0002172 AUCAUAGAggaaaauccauguu 371 hsa-miR-483-5p MIMAT0004761 AAGACGGGaggaaagaagggag 372 hsa-miR-483-3p MIMAT0002173 UCACUCCUcuccucccgucuu 373 hsa-miR-484 MIMAT0002174 UCAGGCUCaguccccucccgau 374 hsa-miR-485-5p MIMAT0002175 AGAGGCUGgccgugaugaauuc 375 hsa-miR-485-3p MIMAT0002176 GUCAUACAcggcucuccucucu 376 hsa-miR-486-5p MIMAT0002177 UCCUGUACugagcugccccgag 377 hsa-miR-486-3p MIMAT0004762 CGGGGCAGcucaguacaggau 378 hsa-miR-487a MIMAT0002178 AAUCAUACagggacauccaguu 379 hsa-miR-488* MIMAT0002804 CCCAGAUAauggcacucucaa 380 hsa-miR-488 MIMAT0004763 UUGAAAGGcuauuucuugguc 381 hsa-miR-489 MIMAT0002805 GUGACAUCacauauacggcagc 382 hsa-miR-490-5p MIMAT0004764 CCAUGGAUcuccaggugggu 383 hsa-miR-490-3p MIMAT0002806 CAACCUGGaggacuccaugcug 384 hsa-miR-491-5p MIMAT0002807 AGUGGGGAacccuuccaugagg 385 hsa-miR-491-3p MIMAT0004765 CUUAUGCAagauucccuucuac 386 hsa-miR-511 MIMAT0002808 GUGUCUUUugcucugcaguca 387 hsa-miR-146b-5p MIMAT0002809 UGAGAACUgaauuccauaggcu 388 hsa-miR-146b-3p MIMAT0004766 UGCCCUGUggacucaguucugg 389 hsa-miR-202* MIMAT0002810 UUCCUAUGcauauacuucuuug 390 hsa-miR-202 MIMAT0002811 AGAGGUAUagggcaugggaa 391 hsa-miR-492 MIMAT0002812 AGGACCUGcgggacaagauucuu 392 hsa-miR-493* MIMAT0002813 UUGUACAUgguaggcuuucauu 393 hsa-miR-493 MIMAT0003161 UGAAGGUCuacugugugccagg 394 hsa-miR-432 MIMAT0002814 UCUUGGAGuaggucauugggugg 395 hsa-miR-432* MIMAT0002815 CUGGAUGGcuccuccaugucu 396 hsa-miR-494 MIMAT0002816 UGAAACAUacacgggaaaccuc 397 hsa-miR-495 MIMAT0002817 AAACAAACauggugcacuucuu 398 hsa-miR-496 MIMAT0002818 UGAGUAUUacauggccaaucuc 399 hsa-miR-193b* MIMAT0004767 CGGGGUUUugagggcgagauga 400 hsa-miR-193b MIMAT0002819 AACUGGCCcucaaagucccgcu 401 hsa-miR-497 MIMAT0002820 CAGCAGCAcacugugguuugu 402 hsa-miR-497* MIMAT0004768 CAAACCACacugugguguuaga 403 hsa-miR-181d MIMAT0002821 AACAUUCAuuguugucggugggu 404 hsa-miR-512-5p MIMAT0002822 CACUCAGCcuugagggcacuuuc 405 hsa-miR-512-3p MIMAT0002823 AAGUGCUGucauagcugagguc 406 hsa-miR-498 MIMAT0002824 UUUCAAGCcagggggcguuuuuc 407 hsa-miR-520e MIMAT0002825 AAAGUGCUuccuuuuugaggg 408 hsa-miR-515-5p MIMAT0002826 UUCUCCAAaagaaagcacuuucug 409 hsa-miR-515-3p MIMAT0002827 GAGUGCCUucuuuuggagcguu 410 hsa-miR-519e* MIMAT0002828 UUCUCCAAaagggagcacuuuc 411 hsa-miR-519e MIMAT0002829 AAGUGCCUccuuuuagaguguu 412 hsa-miR-520f MIMAT0002830 AAGUGCUUccuuuuagaggguu 413 hsa-miR-519c-5p MIMAT0002831 CUCUAGAGggaagcgcuuucug 414 hsa-miR-519c-3p MIMAT0002832 AAAGUGCAucuuuuuagaggau 415 hsa-miR-520a-5p MIMAT0002833 CUCCAGAGggaaguacuuucu 416 hsa-miR-520a-3p MIMAT0002834 AAAGUGCUucccuuuggacugu 417 hsa-miR-526b MIMAT0002835 CUCUUGAGggaagcacuuucugu 418 hsa-miR-526b* MIMAT0002836 GAAAGUGCuuccuuuuagaggc 419 hsa-miR-519b-5p MIMAT0005454 CUCUAGAGggaagcgcuuucug 414 hsa-miR-519b-3p MIMAT0002837 AAAGUGCAuccuuuuagagguu 420 hsa-miR-525-5p MIMAT0002838 CUCCAGAGggaugcacuuucu 421 hsa-miR-525-3p MIMAT0002839 GAAGGCGCuucccuuuagagcg 422 hsa-miR-523* MIMAT0005449 CUCUAGAGggaagcgcuuucug 414 hsa-miR-523 MIMAT0002840 GAACGCGCuucccuauagagggu 423 hsa-miR-518f* MIMAT0002841 CUCUAGAGggaagcacuuucuc 424 hsa-miR-518f MIMAT0002842 GAAAGCGCuucucuuuagagg 425 hsa-miR-520b MIMAT0002843 AAAGUGCUuccuuuuagaggg 426 hsa-miR-518b MIMAT0002844 CAAAGCGCuccccuuuagaggu 427 hsa-miR-526a MIMAT0002845 CUCUAGAGggaagcacuuucug 428 hsa-miR-520c-5p MIMAT0005455 CUCUAGAGggaagcacuuucug 428 hsa-miR-520c-3p MIMAT0002846 AAAGUGCUuccuuuuagagggu 429 hsa-miR-518c* MIMAT0002847 UCUCUGGAgggaagcacuuucug 430 hsa-miR-518c MIMAT0002848 CAAAGCGCuucucuuuagagugu 431 hsa-miR-524-5p MIMAT0002849 CUACAAAGggaagcacuuucuc 432 hsa-miR-524-3p MIMAT0002850 GAAGGCGCuucccuuuggagu 433 hsa-miR-517* MIMAT0002851 CCUCUAGAuggaagcacugucu 434 hsa-miR-517a MIMAT0002852 AUCGUGCAucccuuuagagugu 435 hsa-miR-519d MIMAT0002853 CAAAGUGCcucccuuuagagug 436 hsa-miR-521 MIMAT0002854 AACGCACUucccuuuagagugu 437 hsa-miR-520d-5p MIMAT0002855 CUACAAAGggaagcccuuuc 438 hsa-miR-520d-3p MIMAT0002856 AAAGUGCUucucuuuggugggu 439 hsa-miR-517b MIMAT0002857 UCGUGCAUcccuuuagaguguu 440 hsa-miR-520g MIMAT0002858 ACAAAGUGcuucccuuuagagugu 441 hsa-miR-516b MIMAT0002859 AUCUGGAGguaagaagcacuuu 442 hsa-miR-516b* MIMAT0002860 UGCUUCCUuucagagggu 443 hsa-miR-518e* MIMAT0005450 CUCUAGAGggaagcgcuuucug 414 hsa-miR-518e MIMAT0002861 AAAGCGCUucccuucagagug 444 hsa-miR-518a-5p MIMAT0005457 CUGCAAAGggaagcccuuuc 445 hsa-miR-518a-3p MIMAT0002863 GAAAGCGCuucccuuugcugga 446 hsa-miR-518d-5p MIMAT0005456 CUCUAGAGggaagcacuuucug 428 hsa-miR-518d-3p MIMAT0002864 CAAAGCGCuucccuuuggagc 447 hsa-miR-517c MIMAT0002866 AUCGUGCAuccuuuuagagugu 448 hsa-miR-520h MIMAT0002867 ACAAAGUGcuucccuuuagagu 449 hsa-miR-522* MIMAT0005451 CUCUAGAGggaagcgcuuucug 414 hsa-miR-522 MIMAT0002868 AAAAUGGUucccuuuagagugu 450 hsa-miR-519a* MIMAT0005452 CUCUAGAGggaagcgcuuucug 414 hsa-miR-519a MIMAT0002869 AAAGUGCAuccuuuuagagugu 451 hsa-miR-527 MIMAT0002862 CUGCAAAGggaagcccuuuc 445 hsa-miR-516a-5p MIMAT0004770 UUCUCGAGgaaagaagcacuuuc 452 hsa-miR-516a-3p MIMAT0006778 UGCUUCCUuucagagggu 443 hsa-miR-499-5p MIMAT0002870 UUAAGACUugcagugauguuu 453 hsa-miR-499-3p MIMAT0004772 AACAUCACagcaagucugugcu 454 hsa-miR-500 MIMAT0004773 UAAUCCUUgcuaccugggugaga 455 hsa-miR-500* MIMAT0002871 AUGCACCUgggcaaggauucug 456 hsa-miR-501-5p MIMAT0002872 AAUCCUUUgucccugggugaga 457 hsa-miR-501-3p MIMAT0004774 AAUGCACCcgggcaaggauucu 458 hsa-miR-502-5p MIMAT0002873 AUCCUUGCuaucugggugcua 459 hsa-miR-502-3p MIMAT0004775 AAUGCACCugggcaaggauuca 460 hsa-miR-503 MIMAT0002874 UAGCAGCGggaacaguucugcag 461 hsa-miR-504 MIMAT0002875 AGACCCUGgucugcacucuauc 462 hsa-miR-505* MIMAT0004776 GGGAGCCAggaaguauugaugu 463 hsa-miR-505 MIMAT0002876 CGUCAACAcuugcugguuuccu 464 hsa-miR-513a-5p MIMAT0002877 UUCACAGGgaggugucau 465 hsa-miR-513a-3p MIMAT0004777 UAAAUUUCaccuuucugagaagg 466 hsa-miR-506 MIMAT0002878 UAAGGCACccuucugaguaga 467 hsa-miR-507 MIMAT0002879 UUUUGCACcuuuuggagugaa 468 hsa-miR-508-5p MIMAT0004778 UACUCCAGagggcgucacucaug 469 hsa-miR-508-3p MIMAT0002880 UGAUUGUAgccuuuuggaguaga 470 hsa-miR-509-5p MIMAT0004779 UACUGCAGacaguggcaauca 471 hsa-miR-509-3p MIMAT0002881 UGAUUGGUacgucuguggguag 472 hsa-miR-510 MIMAT0002882 UACUCAGGagaguggcaaucac 473 hsa-miR-514 MIMAT0002883 AUUGACACuucugugaguaga 474 hsa-miR-532-5p MIMAT0002888 CAUGCCUUgaguguaggaccgu 475 hsa-miR-532-3p MIMAT0004780 CCUCCCACacccaaggcuugca 476 hsa-miR-455-5p MIMAT0003150 UAUGUGCCuuuggacuacaucg 477 hsa-miR-455-3p MIMAT0004784 GCAGUCCAugggcauauacac 478 hsa-miR-539 MIMAT0003163 GGAGAAAUuauccuuggugugu 479 hsa-miR-544 MIMAT0003164 AUUCUGCAuuuuuagcaaguuc 480 hsa-miR-545* MIMAT0004785 UCAGUAAAuguuuauuagauga 481 hsa-miR-545 MIMAT0003165 UCAGCAAAcauuuauugugugc 482 hsa-miR-487b MIMAT0003180 AAUCGUACagggucauccacuu 483 hsa-miR-551a MIMAT0003214 GCGACCCAcucuugguuucca 484 hsa-miR-552 MIMAT0003215 AACAGGUGacugguuagacaa 485 hsa-miR-553 MIMAT0003216 AAAACGGUgagauuuuguuuu 486 hsa-miR-554 MIMAT0003217 GCUAGUCCugacucagccagu 487 hsa-miR-92b* MIMAT0004792 AGGGACGGgacgcggugcagug 488 hsa-miR-92b MIMAT0003218 UAUUGCACucgucccggccucc 489 hsa-miR-555 MIMAT0003219 AGGGUAAGcugaaccucugau 490 hsa-miR-556-5p MIMAT0003220 GAUGAGCUcauuguaauaugag 491 hsa-miR-556-3p MIMAT0004793 AUAUUACCauuagcucaucuuu 492 hsa-miR-557 MIMAT0003221 GUUUGCACgggugggccuugucu 493 hsa-miR-558 MIMAT0003222 UGAGCUGCuguaccaaaau 494 hsa-miR-559 MIMAT0003223 UAAAGUAAauaugcaccaaaa 495 hsa-miR-561 MIMAT0003225 CAAAGUUUaagauccuugaagu 496 hsa-miR-562 MIMAT0003226 AAAGUAGCuguaccauuugc 497 hsa-miR-563 MIMAT0003227 AGGUUGACauacguuuccc 498 hsa-miR-564 MIMAT0003228 AGGCACGGugucagcaggc 499 hsa-miR-566 MIMAT0003230 GGGCGCCUgugaucccaac 500 hsa-miR-567 MIMAT0003231 AGUAUGUUcuuccaggacagaac 501 hsa-miR-568 MIMAT0003232 AUGUAUAAauguauacacac 502 hsa-miR-551b* MIMAT0004794 GAAAUCAAgcgugggugagacc 503 hsa-miR-551b MIMAT0003233 GCGACCCAuacuugguuucag 504 hsa-miR-569 MIMAT0003234 AGUUAAUGaauccuggaaagu 505 hsa-miR-570 MIMAT0003235 CGAAAACAgcaauuaccuuugc 506 hsa-miR-571 MIMAT0003236 UGAGUUGGccaucugagugag 507 hsa-miR-572 MIMAT0003237 GUCCGCUCggcgguggccca 508 hsa-miR-573 MIMAT0003238 CUGAAGUGauguguaacugaucag 509 hsa-miR-574-5p MIMAT0004795 UGAGUGUGugugugugagugugu 510 hsa-miR-574-3p MIMAT0003239 CACGCUCAugcacacacccaca 511 hsa-miR-575 MIMAT0003240 GAGCCAGUuggacaggagc 512 hsa-miR-576-5p MIMAT0003241 AUUCUAAUuucuccacgucuuu 513 hsa-miR-576-3p MIMAT0004796 AAGAUGUGgaaaaauuggaauc 514 hsa-miR-577 MIMAT0003242 UAGAUAAAauauugguaccug 515 hsa-miR-578 MIMAT0003243 CUUCUUGUgcucuaggauugu 516 hsa-miR-579 MIMAT0003244 UUCAUUUGguauaaaccgcgauu 517 hsa-miR-580 MIMAT0003245 UUGAGAAUgaugaaucauuagg 518 hsa-miR-581 MIMAT0003246 UCUUGUGUucucuagaucagu 519 hsa-miR-582-5p MIMAT0003247 UUACAGUUguucaaccaguuacu 520 hsa-miR-582-3p MIMAT0004797 UAACUGGUugaacaacugaacc 521 hsa-miR-583 MIMAT0003248 CAAAGAGGaaggucccauuac 522 hsa-miR-584 MIMAT0003249 UUAUGGUUugccugggacugag 523 hsa-miR-585 MIMAT0003250 UGGGCGUAucuguaugcua 524 hsa-miR-548a-3p MIMAT0003251 CAAAACUGgcaauuacuuuugc 525 hsa-miR-586 MIMAT0003252 UAUGCAUUguauuuuuaggucc 526 hsa-miR-587 MIMAT0003253 UUUCCAUAggugaugagucac 527 hsa-miR-548b-5p MIMAT0004798 AAAAGUAAuugugguuuuggcc 528 hsa-miR-548b-3p MIMAT0003254 CAAGAACCucaguugcuuuugu 529 hsa-miR-588 MIMAT0003255 UUGGCCACaauggguuagaac 530 hsa-miR-589 MIMAT0004799 UGAGAACCacgucugcucugag 531 hsa-miR-589* MIMAT0003256 UCAGAACAaaugccgguucccaga 532 hsa-miR-550 MIMAT0004800 AGUGCCUGagggaguaagagccc 533 hsa-miR-550* MIMAT0003257 UGUCUUACucccucaggcacau 534 hsa-miR-590-5p MIMAT0003258 GAGCUUAUucauaaaagugcag 535 hsa-miR-590-3p MIMAT0004801 UAAUUUUAuguauaagcuagu 536 hsa-miR-591 MIMAT0003259 AGACCAUGgguucucauugu 537 hsa-miR-592 MIMAT0003260 UUGUGUCAauaugcgaugaugu 538 hsa-miR-593* MIMAT0003261 AGGCACCAgccaggcauugcucagc 539 hsa-miR-593 MIMAT0004802 UGUCUCUGcugggguuucu 540 hsa-miR-595 MIMAT0003263 GAAGUGUGccguggugugucu 541 hsa-miR-596 MIMAT0003264 AAGCCUGCccggcuccucggg 542 hsa-miR-597 MIMAT0003265 UGUGUCACucgaugaccacugu 543 hsa-miR-598 MIMAT0003266 UACGUCAUcguugucaucguca 544 hsa-miR-599 MIMAT0003267 GUUGUGUCaguuuaucaaac 545 hsa-miR-548a-5p MIMAT0004803 AAAAGUAAuugcgaguuuuacc 546 hsa-miR-600 MIMAT0003268 ACUUACAGacaagagccuugcuc 547 hsa-miR-601 MIMAT0003269 UGGUCUAGgauuguuggaggag 548 hsa-miR-602 MIMAT0003270 GACACGGGcgacagcugcggccc 549 hsa-miR-603 MIMAT0003271 CACACACUgcaauuacuuuugc 550 hsa-miR-604 MIMAT0003272 AGGCUGCGgaauucaggac 551 hsa-miR-605 MIMAT0003273 UAAAUCCCauggugccuucuccu 552 hsa-miR-606 MIMAT0003274 AAACUACUgaaaaucaaagau 553 hsa-miR-607 MIMAT0003275 GUUCAAAUccagaucuauaac 554 hsa-miR-608 MIMAT0003276 AGGGGUGGuguugggacagcuccgu 555 hsa-miR-609 MIMAT0003277 AGGGUGUUucucucaucucu 556 hsa-miR-610 MIMAT0003278 UGAGCUAAaugugugcuggga 557 hsa-miR-611 MIMAT0003279 GCGAGGACcccucggggucugac 558 hsa-miR-612 MIMAT0003280 GCUGGGCAgggcuucugagcuccuu 559 hsa-miR-613 MIMAT0003281 AGGAAUGUuccuucuuugcc 560 hsa-miR-614 MIMAT0003282 GAACGCCUguucuugccaggugg 561 hsa-miR-615-5p MIMAT0004804 GGGGGUCCccggugcucggauc 562 hsa-miR-615-3p MIMAT0003283 UCCGAGCCugggucucccucuu 563 hsa-miR-616* MIMAT0003284 ACUCAAAAcccuucagugacuu 564 hsa-miR-616 MIMAT0004805 AGUCAUUGgaggguuugagcag 565 hsa-miR-548c-5p MIMAT0004806 AAAAGUAAuugcgguuuuugcc 566 hsa-miR-548c-3p MIMAT0003285 CAAAAAUCucaauuacuuuugc 567 hsa-miR-617 MIMAT0003286 AGACUUCCcauuugaagguggc 568 hsa-miR-618 MIMAT0003287 AAACUCUAcuuguccuucugagu 569 hsa-miR-619 MIMAT0003288 GACCUGGAcauguuugugcccagu 570 hsa-miR-620 MIMAT0003289 AUGGAGAUagauauagaaau 571 hsa-miR-621 MIMAT0003290 GGCUAGCAacagcgcuuaccu 572 hsa-miR-622 MIMAT0003291 ACAGUCUGcugagguuggagc 573 hsa-miR-623 MIMAT0003292 AUCCCUUGcaggggcuguugggu 574 hsa-miR-624* MIMAT0003293 UAGUACCAguaccuuguguuca 575 hsa-miR-624 MIMAT0004807 CACAAGGUauugguauuaccu 576 hsa-miR-625 MIMAT0003294 AGGGGGAAaguucuauagucc 577 hsa-miR-625* MIMAT0004808 GACUAUAGaacuuucccccuca 578 hsa-miR-626 MIMAT0003295 AGCUGUCUgaaaaugucuu 579 hsa-miR-627 MIMAT0003296 GUGAGUCUcuaagaaaagagga 580 hsa-miR-628-5p MIMAT0004809 AUGCUGACauauuuacuagagg 581 hsa-miR-628-3p MIMAT0003297 UCUAGUAAgaguggcagucga 582 hsa-miR-629 MIMAT0004810 UGGGUUUAcguugggagaacu 583 hsa-miR-629* MIMAT0003298 GUUCUCCCaacguaagcccagc 584 hsa-miR-630 MIMAT0003299 AGUAUUCUguaccagggaaggu 585 hsa-miR-631 MIMAT0003300 AGACCUGGcccagaccucagc 586 hsa-miR-33b MIMAT0003301 GUGCAUUGcuguugcauugc 587 hsa-miR-33b* MIMAT0004811 CAGUGCCUcggcagugcagccc 588 hsa-miR-632 MIMAT0003302 GUGUCUGCuuccuguggga 589 hsa-miR-633 MIMAT0003303 CUAAUAGUaucuaccacaauaaa 590 hsa-miR-634 MIMAT0003304 AACCAGCAccccaacuuuggac 591 hsa-miR-635 MIMAT0003305 ACUUGGGCacugaaacaaugucc 592 hsa-miR-636 MIMAT0003306 UGUGCUUGcucgucccgcccgca 593 hsa-miR-637 MIMAT0003307 ACUGGGGGcuuucgggcucugcgu 594 hsa-miR-638 MIMAT0003308 AGGGAUCGcgggcggguggcggccu 595 hsa-miR-639 MIMAT0003309 AUCGCUGCgguugcgagcgcugu 596 hsa-miR-640 MIMAT0003310 AUGAUCCAggaaccugccucu 597 hsa-miR-641 MIMAT0003311 AAAGACAUaggauagagucaccuc 598 hsa-miR-642 MIMAT0003312 GUCCCUCUccaaaugugucuug 599 hsa-miR-643 MIMAT0003313 ACUUGUAUgcuagcucagguag 600 hsa-miR-644 MIMAT0003314 AGUGUGGCuuucuuagagc 601 hsa-miR-645 MIMAT0003315 UCUAGGCUgguacugcuga 602 hsa-miR-646 MIMAT0003316 AAGCAGCUgccucugaggc 603 hsa-miR-647 MIMAT0003317 GUGGCUGCacucacuuccuuc 604 hsa-miR-648 MIMAT0003318 AAGUGUGCagggcacuggu 605 hsa-miR-649 MIMAT0003319 AAACCUGUguuguucaagaguc 606 hsa-miR-650 MIMAT0003320 AGGAGGCAgcgcucucaggac 607 hsa-miR-651 MIMAT0003321 UUUAGGAUaagcuugacuuuug 608 hsa-miR-652 MIMAT0003322 AAUGGCGCcacuaggguugug 609 hsa-miR-548d-5p MIMAT0004812 AAAAGUAAuugugguuuuugcc 610 hsa-miR-548d-3p MIMAT0003323 CAAAAACCacaguuucuuuugc 611 hsa-miR-661 MIMAT0003324 UGCCUGGGucucuggccugcgcgu 612 hsa-miR-662 MIMAT0003325 UCCCACGUuguggcccagcag 613 hsa-miR-663 MIMAT0003326 AGGCGGGGcgccgcgggaccgc 614 hsa-miR-449b MIMAT0003327 AGGCAGUGuauuguuagcuggc 615 hsa-miR-449b* MIMAT0009203 CAGCCACAacuacccugccacu 616 hsa-miR-653 MIMAT0003328 GUGUUGAAacaaucucuacug 617 hsa-miR-411 MIMAT0003329 UAGUAGACcguauagcguacg 618 hsa-miR-411* MIMAT0004813 UAUGUAACacgguccacuaacc 619 hsa-miR-654-5p MIMAT0003330 UGGUGGGCcgcagaacaugugc 620 hsa-miR-654-3p MIMAT0004814 UAUGUCUGcugaccaucaccuu 621 hsa-miR-655 MIMAT0003331 AUAAUACAugguuaaccucuuu 622 hsa-miR-656 MIMAT0003332 AAUAUUAUacagucaaccucu 623 hsa-miR-549 MIMAT0003333 UGACAACUauggaugagcucu 624 hsa-miR-657 MIMAT0003335 GGCAGGUUcucacccucucuagg 625 hsa-miR-658 MIMAT0003336 GGCGGAGGgaaguagguccguuggu 626 hsa-miR-659 MIMAT0003337 CUUGGUUCagggagggucccca 627 hsa-miR-660 MIMAT0003338 UACCCAUUgcauaucggaguug 628 hsa-miR-421 MIMAT0003339 AUCAACAGacauuaauugggcgc 629 hsa-miR-542-5p MIMAT0003340 UCGGGGAUcaucaugucacgaga 630 hsa-miR-542-3p MIMAT0003389 UGUGACAGauugauaacugaaa 631 hsa-miR-758 MIMAT0003879 UUUGUGACcugguccacuaacc 632 hsa-miR-1264 MIMAT0005791 CAAGUCUUauuugagcaccuguu 633 hsa-miR-671-5p MIMAT0003880 AGGAAGCCcuggaggggcuggag 634 hsa-miR-671-3p MIMAT0004819 UCCGGUUCucagggcuccacc 635 hsa-miR-668 MIMAT0003881 UGUCACUCggcucggcccacuac 636 hsa-miR-767-5p MIMAT0003882 UGCACCAUgguugucugagcaug 637 hsa-miR-767-3p MIMAT0003883 UCUGCUCAuaccccaugguuucu 638 hsa-miR-1224-5p MIMAT0005458 GUGAGGACucgggaggugg 639 hsa-miR-1224-3p MIMAT0005459 CCCCACCUccucucuccucag 640 hsa-miR-320b MIMAT0005792 AAAAGCUGgguugagagggcaa 641 hsa-miR-320c MIMAT0005793 AAAAGCUGgguugagagggu 642 hsa-miR-1296 MIMAT0005794 UUAGGGCCcuggcuccaucucc 643 hsa-miR-1468 MIMAT0006789 CUCCGUUUgccuguuucgcug 644 hsa-miR-1323 MIMAT0005795 UCAAAACUgaggggcauuuucu 645 hsa-miR-1271 MIMAT0005796 CUUGGCACcuagcaagcacuca 646 hsa-miR-1301 MIMAT0005797 UUGCAGCUgccugggagugacuuc 647 hsa-miR-454* MIMAT0003884 ACCCUAUCaauauugucucugc 648 hsa-miR-454 MIMAT0003885 UAGUGCAAuauugcuuauagggu 649 hsa-miR-1185 MIMAT0005798 AGAGGAUAcccuuuguauguu 650 hsa-miR-449c MIMAT0010251 UAGGCAGUguauugcuagcggcugu 651 hsa-miR-449c* MIMAT0013771 UUGCUAGUugcacuccucucugu 652 hsa-miR-1283 MIMAT0005799 UCUACAAAggaaagcgcuuucu 653 hsa-miR-769-5p MIMAT0003886 UGAGACCUcuggguucugagcu 654 hsa-miR-769-3p MIMAT0003887 CUGGGAUCuccggggucuugguu 655 hsa-miR-766 MIMAT0003888 ACUCCAGCcccacagccucagc 656 hsa-miR-762 MIMAT0010313 GGGGCUGGggccggggccgagc 657 hsa-miR-802 MIMAT0004185 CAGUAACAaagauucauccuugu 658 hsa-miR-670 MIMAT0010357 GUCCCUGAguguauguggug 659 hsa-miR-1298 MIMAT0005800 UUCAUUCGgcuguccagaugua 660 hsa-miR-2113 MIMAT0009206 AUUUGUGCuuggcucugucac 661 hsa-miR-761 MIMAT0010364 GCAGCAGGgugaaacugacaca 662 hsa-miR-764 MIMAT0010367 GCAGGUGCucacuuguccuccu 663 hsa-miR-759 MIMAT0010497 GCAGAGUGcaaacaauuuugac 664 hsa-miR-765 MIMAT0003945 UGGAGGAGaaggaaggugaug 665 hsa-miR-770-5p MIMAT0003948 UCCAGUACcacgugucagggcca 666 hsa-miR-675 MIMAT0004284 UGGUGCGGagagggcccacagug 667 hsa-miR-675* MIMAT0006790 CUGUAUGCccucaccgcuca 668 hsa-miR-298 MIMAT0004901 AGCAGAAGcagggagguucuccca 669 hsa-miR-891a MIMAT0004902 UGCAACGAaccugagccacuga 670 hsa-miR-300 MIMAT0004903 UAUACAAGggcagacucucucu 671 hsa-miR-886-5p MIMAT0004905 CGGGUCGGaguuagcucaagcgg 672 hsa-miR-886-3p MIMAT0004906 CGCGGGUGcuuacugacccuu 673 hsa-miR-892a MIMAT0004907 CACUGUGUccuuucugcguag 674 hsa-miR-220b MIMAT0004908 CCACCACCgugucugacacuu 675 hsa-miR-450b-5p MIMAT0004909 UUUUGCAAuauguuccugaaua 676 hsa-miR-450b-3p MIMAT0004910 UUGGGAUCauuuugcauccaua 677 hsa-miR-874 MIMAT0004911 CUGCCCUGgcccgagggaccga 678 hsa-miR-890 MIMAT0004912 UACUUGGAaaggcaucaguug 679 hsa-miR-891b MIMAT0004913 UGCAACUUaccugagucauuga 680 hsa-miR-220c MIMAT0004915 ACACAGGGcuguugugaagacu 681 hsa-miR-888 MIMAT0004916 UACUCAAAaagcugucaguca 682 hsa-miR-888* MIMAT0004917 GACUGACAccucuuugggugaa 683 hsa-miR-892b MIMAT0004918 CACUGGCUccuuucuggguaga 684 hsa-miR-541* MIMAT0004919 AAAGGAUUcugcugucggucccacu 685 hsa-miR-541 MIMAT0004920 UGGUGGGCacagaaucuggacu 686 hsa-miR-889 MIMAT0004921 UUAAUAUCggacaaccauugu 687 hsa-miR-875-5p MIMAT0004922 UAUACCUCaguuuuaucaggug 688 hsa-miR-875-3p MIMAT0004923 CCUGGAAAcacugagguugug 689 hsa-miR-876-5p MIMAT0004924 UGGAUUUCuuugugaaucacca 690 hsa-miR-876-3p MIMAT0004925 UGGUGGUUuacaaaguaauuca 691 hsa-miR-708 MIMAT0004926 AAGGAGCUuacaaucuagcuggg 692 hsa-miR-708* MIMAT0004927 CAACUAGAcugugagcuucuag 693 hsa-miR-147b MIMAT0004928 GUGUGCGGaaaugcuucugcua 694 hsa-miR-190b MIMAT0004929 UGAUAUGUuugauauuggguu 695 hsa-miR-744 MIMAT0004945 UGCGGGGCuagggcuaacagca 696 hsa-miR-744* MIMAT0004946 CUGUUGCCacuaaccucaaccu 697 hsa-miR-885-5p MIMAT0004947 UCCAUUACacuacccugccucu 698 hsa-miR-885-3p MIMAT0004948 AGGCAGCGggguguaguggaua 699 hsa-miR-877 MIMAT0004949 GUAGAGGAgauggcgcaggg 700 hsa-miR-877* MIMAT0004950 UCCUCUUCucccuccucccag 701 hsa-miR-887 MIMAT0004951 GUGAACGGgcgccaucccgagg 702 hsa-miR-665 MIMAT0004952 ACCAGGAGgcugaggccccu 703 hsa-miR-873 MIMAT0004953 GCAGGAACuugugagucuccu 704 hsa-miR-543 MIMAT0004954 AAACAUUCgcggugcacuucuu 705 hsa-miR-374b MIMAT0004955 AUAUAAUAcaaccugcuaagug 706 hsa-miR-374b* MIMAT0004956 CUUAGCAGguuguauuaucauu 707 hsa-miR-760 MIMAT0004957 CGGCUCUGggucugugggga 708 hsa-miR-301b MIMAT0004958 CAGUGCAAugauauugucaaagc 709 hsa-miR-216b MIMAT0004959 AAAUCUCUgcaggcaaauguga 710 hsa-miR-208b MIMAT0004960 AUAAGACGaacaaaagguuugu 711 hsa-miR-920 MIMAT0004970 GGGGAGCUguggaagcagua 712 hsa-miR-921 MIMAT0004971 CUAGUGAGggacagaaccaggauuc 713 hsa-miR-922 MIMAT0004972 GCAGCAGAgaauaggacuacguc 714 hsa-miR-924 MIMAT0004974 AGAGUCUUgugaugucuugc 715 hsa-miR-509-3-5p MIMAT0004975 UACUGCAGacguggcaaucaug 716 hsa-miR-933 MIMAT0004976 UGUGCGCAgggagaccucuccc 717 hsa-miR-934 MIMAT0004977 UGUCUACUacuggagacacugg 718 hsa-miR-935 MIMAT0004978 CCAGUUACcgcuuccgcuaccgc 719 hsa-miR-936 MIMAT0004979 ACAGUAGAgggaggaaucgcag 720 hsa-miR-937 MIMAT0004980 AUCCGCGCucugacucucugcc 721 hsa-miR-938 MIMAT0004981 UGCCCUUAaaggugaacccagu 722 hsa-miR-939 MIMAT0004982 UGGGGAGCugaggcucugggggug 723 hsa-miR-940 MIMAT0004983 AAGGCAGGgcccccgcucccc 724 hsa-miR-941 MIMAT0004984 CACCCGGCugugugcacaugugc 725 hsa-miR-942 MIMAT0004985 UCUUCUCUguuuuggccaugug 726 hsa-miR-943 MIMAT0004986 CUGACUGUugccguccuccag 727 hsa-miR-944 MIMAT0004987 AAAUUAUUguacaucggaugag 728 hsa-miR-297 MIMAT0004450 AUGUAUGUgugcaugugcaug 729 hsa-miR-1178 MIMAT0005823 UUGCUCACuguucuucccuag 730 hsa-miR-1179 MIMAT0005824 AAGCAUUCuuucauugguugg 731 hsa-miR-1180 MIMAT0005825 UUUCCGGCucgcgugggugugu 732 hsa-miR-1181 MIMAT0005826 CCGUCGCCgccacccgagccg 733 hsa-miR-1182 MIMAT0005827 GAGGGUCUugggagggaugugac 734 hsa-miR-1183 MIMAT0005828 CACUGUAGgugauggugagagugggca 735 hsa-miR-1184 MIMAT0005829 CCUGCAGCgacuugauggcuucc 736 hsa-miR-1225-5p MIMAT0005572 GUGGGUACggcccagugggggg 737 hsa-miR-1225-3p MIMAT0005573 UGAGCCCCugugccgcccccag 738 hsa-miR-1226* MIMAT0005576 GUGAGGGCaugcaggccuggaugggg 739 hsa-miR-1226 MIMAT0005577 UCACCAGCccuguguucccuag 740 hsa-miR-1227 MIMAT0005580 CGUGCCACccuuuuccccag 741 hsa-miR-1228* MIMAT0005582 GUGGGCGGgggcaggugugug 742 hsa-miR-1228 MIMAT0005583 UCACACCUgccucgcccccc 743 hsa-miR-1229 MIMAT0005584 CUCUCACCacugcccucccacag 744 hsa-miR-1231 MIMAT0005586 GUGUCUGGgcggacagcugc 745 hsa-miR-1233 MIMAT0005588 UGAGCCCUguccucccgcag 746 hsa-miR-1234 MIMAT0005589 UCGGCCUGaccacccaccccac 747 hsa-miR-1236 MIMAT0005591 CCUCUUCCccuugucucuccag 748 hsa-miR-1237 MIMAT0005592 UCCUUCUGcuccgucccccag 749 hsa-miR-1238 MIMAT0005593 CUUCCUCGucugucugcccc 750 hsa-miR-1200 MIMAT0005863 CUCCUGAGccauucugagccuc 751 hsa-miR-1201 MIMAT0005864 AGCCUGAUuaaacacaugcucuga 752 hsa-miR-1202 MIMAT0005865 GUGCCAGCugcagugggggag 753 hsa-miR-1203 MIMAT0005866 CCCGGAGCcaggaugcagcuc 754 hsa-miR-663b MIMAT0005867 GGUGGCCCggccgugccugagg 755 hsa-miR-1204 MIMAT0005868 UCGUGGCCuggucuccauuau 756 hsa-miR-1205 MIMAT0005869 UCUGCAGGguuugcuuugag 757 hsa-miR-1206 MIMAT0005870 UGUUCAUGuagauguuuaagc 758 hsa-miR-1207-5p MIMAT0005871 UGGCAGGGaggcugggagggg 759 hsa-miR-1207-3p MIMAT0005872 UCAGCUGGcccucauuuc 760 hsa-miR-1208 MIMAT0005873 UCACUGUUcagacaggcgga 761 hsa-miR-548e MIMAT0005874 AAAAACUGagacuacuuuugca 762 hsa-miR-548j MIMAT0005875 AAAAGUAAuugcggucuuuggu 763 hsa-miR-1285 MIMAT0005876 UCUGGGCAacaaagugagaccu 764 hsa-miR-1286 MIMAT0005877 UGCAGGACcaagaugagcccu 765 hsa-miR-1287 MIMAT0005878 UGCUGGAUcagugguucgaguc 766 hsa-miR-1289 MIMAT0005879 UGGAGUCCaggaaucugcauuuu 767 hsa-miR-1290 MIMAT0005880 UGGAUUUUuggaucaggga 768 hsa-miR-1291 MIMAT0005881 UGGCCCUGacugaagaccagcagu 769 hsa-miR-548k MIMAT0005882 AAAAGUACuugcggauuuugcu 770 hsa-miR-1293 MIMAT0005883 UGGGUGGUcuggagauuugugc 771 hsa-miR-1294 MIMAT0005884 UGUGAGGUuggcauuguugucu 772 hsa-miR-1295 MIMAT0005885 UUAGGCCGcagaucuggguga 773 hsa-miR-1297 MIMAT0005886 UUCAAGUAauucaggug 774 hsa-miR-1299 MIMAT0005887 UUCUGGAAuucugugugaggga 775 hsa-miR-5481 MIMAT0005889 AAAAGUAUuugcggguuuuguc 776 hsa-miR-1302 MIMAT0005890 UUGGGACAuacuuaugcuaaa 777 hsa-miR-1303 MIMAT0005891 UUUAGAGAcggggucuugcucu 778 hsa-miR-1304 MIMAT0005892 UUUGAGGCuacagugagaugug 779 hsa-miR-1305 MIMAT0005893 UUUUCAACucuaaugggagaga 780 hsa-miR-1243 MIMAT0005894 AACUGGAUcaauuauaggagug 781 hsa-miR-548f MIMAT0005895 AAAAACUGuaauuacuuuu 782 hsa-miR-1244 MIMAT0005896 AAGUAGUUgguuuguaugagaugguu 783 hsa-miR-1245 MIMAT0005897 AAGUGAUCuaaaggccuacau 784 hsa-miR-1246 MIMAT0005898 AAUGGAUUuuuggagcagg 785 hsa-miR-1247 MIMAT0005899 ACCCGUCCcguucguccccgga 786 hsa-miR-1248 MIMAT0005900 ACCUUCUUguauaagcacugugcuaaa 787 hsa-miR-1249 MIMAT0005901 ACGCCCUUcccccccuucuuca 788 hsa-miR-1250 MIMAT0005902 ACGGUGCUggauguggccuuu 789 hsa-miR-1251 MIMAT0005903 ACUCUAGCugccaaaggcgcu 790 hsa-miR-1253 MIMAT0005904 AGAGAAGAagaucagccugca 791 hsa-miR-1254 MIMAT0005905 AGCCUGGAagcuggagccugcagu 792 hsa-miR-1255a MIMAT0005906 AGGAUGAGcaaagaaaguagauu 793 hsa-miR-1256 MIMAT0005907 AGGCAUUGacuucucacuagcu 794 hsa-miR-1257 MIMAT0005908 AGUGAAUGauggguucugacc 795 hsa-miR-1258 MIMAT0005909 AGUUAGGAuuaggucguggaa 796 hsa-miR-1259 MIMAT0005910 AUAUAUGAugacuuagcuuuu 797 hsa-miR-1260 MIMAT0005911 AUCCCACCucugccacca 798 hsa-miR-548g MIMAT0005912 AAAACUGUaauuacuuuuguac 799 hsa-miR-1261 MIMAT0005913 AUGGAUAAggcuuuggcuu 800 hsa-miR-1262 MIMAT0005914 AUGGGUGAauuuguagaaggau 801 hsa-miR-1263 MIMAT0005915 AUGGUACCcuggcauacugagu 802 hsa-miR-548n MIMAT0005916 CAAAAGUAauuguggauuuugu 803 hsa-miR-548m MIMAT0005917 CAAAGGUAuuugugguuuuug 804 hsa-miR-1265 MIMAT0005918 CAGGAUGUggucaaguguuguu 805 hsa-miR-548o MIMAT0005919 CCAAAACUgcaguuacuuuugc 806 hsa-miR-1266 MIMAT0005920 CCUCAGGGcuguagaacagggcu 807 hsa-miR-1267 MIMAT0005921 CCUGUUGAaguguaaucccca 808 hsa-miR-1268 MIMAT0005922 CGGGCGUGgugguggggg 809 hsa-miR-1269 MIMAT0005923 CUGGACUGagccgugcuacugg 810 hsa-miR-1270 MIMAT0005924 CUGGAGAUauggaagagcugugu 811 hsa-miR-1272 MIMAT0005925 GAUGAUGAuggcagcaaauucugaaa 812 hsa-miR-1273 MIMAT0005926 GGGCGACAaagcaagacucuuucuu 813 hsa-miR-1274a MIMAT0005927 GUCCCUGUucaggcgcca 814 hsa-miR-548h MIMAT0005928 AAAAGUAAucgcgguuuuuguc 815 hsa-miR-1275 MIMAT0005929 GUGGGGGAgaggcuguc 816 hsa-miR-1276 MIMAT0005930 UAAAGAGCccuguggagaca 817 hsa-miR-302e MIMAT0005931 UAAGUGCUuccaugcuu 818 hsa-miR-302f MIMAT0005932 UAAUUGCUuccauguuu 819 hsa-miR-1277 MIMAT0005933 UACGUAGAuauauauguauuuu 820 hsa-miR-548p MIMAT0005934 UAGCAAAAacugcaguuacuuu 821 hsa-miR-548i MIMAT0005935 AAAAGUAAuugcggauuuugcc 822 hsa-miR-1278 MIMAT0005936 UAGUACUGugcauaucaucuau 823 hsa-miR-1279 MIMAT0005937 UCAUAUUGcuucuuucu 824 hsa-miR-1274b MIMAT0005938 UCCCUGUUcgggcgcca 825 hsa-miR-1281 MIMAT0005939 UCGCCUCCuccucuccc 826 hsa-miR-1282 MIMAT0005940 UCGUUUGCcuuuuucugcuu 827 hsa-miR-1284 MIMAT0005941 UCUAUACAgacccuggcuuuuc 828 hsa-miR-1288 MIMAT0005942 UGGACUGCccugaucuggaga 829 hsa-miR-1292 MIMAT0005943 UGGGAACGgguuccggcagacgcug 830 hsa-miR-1252 MIMAT0005944 AGAAGGAAauugaauucauuua 831 hsa-miR-1255b MIMAT0005945 CGGAUGAGcaaagaaagugguu 832 hsa-miR-1280 MIMAT0005946 UCCCACCGcugccaccc 833 hsa-miR-1308 MIMAT0005947 GCAUGGGUgguucagugg 834 hsa-miR-664* MIMAT0005948 ACUGGCUAgggaaaaugauuggau 835 hsa-miR-664 MIMAT0005949 UAUUCAUUuauccccagccuaca 836 hsa-miR-1306 MIMAT0005950 ACGUUGGCucugguggug 837 hsa-miR-1307 MIMAT0005951 ACUCGGCGuggcgucggucgug 838 hsa-miR-513b MIMAT0005788 UUCACAAGgaggugucauuuau 839 hsa-miR-513c MIMAT0005789 UUCUCAAGgaggugucguuuau 840 hsa-miR-1321 MIMAT0005952 CAGGGAGGugaaugugau 841 hsa-miR-1322 MIMAT0005953 GAUGAUGCugcugaugcug 842 hsa-miR-720 MIMAT0005954 UCUCGCUGgggccucca 843 hsa-miR-1197 MIMAT0005955 UAGGACACauggucuacuucu 844 hsa-miR-1324 MIMAT0005956 CCAGACAGaauucuaugcacuuuc 845 hsa-miR-1469 MIMAT0007347 CUCGGCGCggggcgcgggcucc 846 hsa-miR-1470 MIMAT0007348 GCCCUCCGcccgugcaccccg 847 hsa-miR-1471 MIMAT0007349 GCCCGCGUguggagccaggugu 848 hsa-miR-1537 MIMAT0007399 AAAACCGUcuaguuacaguugu 849 hsa-miR-1538 MIMAT0007400 CGGCCCGGgcugcugcuguuccu 850 hsa-miR-1539 MIMAT0007401 UCCUGCGCgucccagaugccc 851 hsa-miR-103-as MIMAT0007402 UCAUAGCCcuguacaaugcugcu 852 hsa-miR-320d MIMAT0006764 AAAAGCUGgguugagagga 853 hsa-miR-1825 MIMAT0006765 UCCAGUGCccuccucucc 854 hsa-miR-1826 MIMAT0006766 AUUGAUCAucgacacuucgaacgcaau 855 hsa-miR-1827 MIMAT0006767 UGAGGCAGuagauugaau 856 hsa-miR-1908 MIMAT0007881 CGGCGGGGacggcgauugguc 857 hsa-miR-1909* MIMAT0007882 UGAGUGCCggugccugcccug 858 hsa-miR-1909 MIMAT0007883 CGCAGGGGccgggugcucaccg 859 hsa-miR-1910 MIMAT0007884 CCAGUCCUgugccugccgccu 860 hsa-miR-1911 MIMAT0007885 UGAGUACCgccaugucuguuggg 861 hsa-miR-1911* MIMAT0007886 CACCAGGCauuguggucucc 862 hsa-miR-1912 MIMAT0007887 UACCCAGAgcaugcagugugaa 863 hsa-miR-1913 MIMAT0007888 UCUGCCCCcuccgcugcugcca 864 hsa-miR-1914 MIMAT0007889 CCCUGUGCccggcccacuucug 865 hsa-miR-1914* MIMAT0007890 GGAGGGGUcccgcacugggagg 866 hsa-miR-1915* MIMAT0007891 ACCUUGCCuugcugcccgggcc 867 hsa-miR-1915 MIMAT0007892 CCCCAGGGcgacgcggcggg 868 hsa-miR-1972 MIMAT0009447 UCAGGCCAggcacaguggcuca 869 hsa-miR-1973 MIMAT0009448 ACCGUGCAaagguagcaua 870 hsa-miR-1975 MIMAT0009450 CCCCCACAaccgcgcuugacuagcu 871 hsa-miR-1976 MIMAT0009451 CCUCCUGCccuccuugcugu 872 hsa-miR-1979 MIMAT0009454 CUCCCACUgcuucacuugacua 873 hsa-miR-2052 MIMAT0009977 UGUUUUGAuaacaguaaugu 874 hsa-miR-2053 MIMAT0009978 GUGUUAAUuaaaccucuauuuac 875 hsa-miR-2054 MIMAT0009979 CUGUAAUAuaaauuuaauuuauu 876 hsa-miR-2110 MIMAT0010133 UUGGGGAAacggccgcugagug 877 hsa-miR-2114 MIMAT0011156 UAGUCCCUuccuugaagcgguc 878 hsa-miR-2114* MIMAT0011157 CGAGCCUCaagcaagggacuu 879 hsa-miR-2115 MIMAT0011158 AGCUUCCAugacuccugaugga 880 hsa-miR-2115* MIMAT0011159 CAUCAGAAuucauggaggcuag 881 hsa-miR-2116 MIMAT0011160 GGUUCUUAgcauaggaggucu 882 hsa-miR-2116* MIMAT0011161 CCUCCCAUgccaagaacuccc 883 hsa-miR-2117 MIMAT0011162 UGUUCUCUuugccaaggacag 884 hsa-miR-548q MIMAT0011163 GCUGGUGCaaaaguaauggcgg 885 hsa-miR-2276 MIMAT0011775 UCUGCAAGugucagaggcgagg 886 hsa-miR-2277 MIMAT0011777 UGACAGCGcccugccuggcuc 887 hsa-miR-2278 MIMAT0011778 GAGAGCAGuguguguugccugg 888 hsa-miR-711 MIMAT0012734 GGGACCCAgggagagacguaag 889 hsa-miR-718 MIMAT0012735 CUUCCGCCccgccgggcgucg 890 hsa-miR-2861 MIMAT0013802 GGGGCCUGgcggugggcgg 891 hsa-miR-2909 MIMAT0013863 GUUAGGGCcaacaucucuugg 892 hsa-miR-3115 MIMAT0014977 AUAUGGGUuuacuaguuggu 893 hsa-miR-3116 MIMAT0014978 UGCCUGGAacauaguagggacu 894 hsa-miR-3117 MIMAT0014979 AUAGGACUcauauagugccag 895 hsa-miR-3118 MIMAT0014980 UGUGACUGcauuaugaaaauucu 896 hsa-miR-3119 MIMAT0014981 UGGCUUUUaacuuugauggc 897 hsa-miR-3120 MIMAT0014982 CACAGCAAguguagacaggca 898 hsa-miR-3121 MIMAT0014983 UAAAUAGAguaggcaaaggaca 899 hsa-miR-3122 MIMAT0014984 GUUGGGACaagaggacggucuu 900 hsa-miR-3123 MIMAT0014985 CAGAGAAUuguuuaauc 901 hsa-miR-3124 MIMAT0014986 UUCGCGGGcgaaggcaaaguc 902 hsa-miR-548s MIMAT0014987 AUGGCCAAaacugcaguuauuuu 903 hsa-miR-3125 MIMAT0014988 UAGAGGAAgcuguggagaga 904 hsa-miR-3126-5p MIMAT0014989 UGAGGGACagaugccagaagca 905 hsa-miR-3126-3p MIMAT0015377 CAUCUGGCauccgucacacaga 906 hsa-miR-3127 MIMAT0014990 AUCAGGGCuuguggaaugggaag 907 hsa-miR-3128 MIMAT0014991 UCUGGCAAguaaaaaacucucau 908 hsa-miR-3129 MIMAT0014992 GCAGUAGUguagagauugguuu 909 hsa-miR-3130-5p MIMAT0014995 UACCCAGUcuccggugcagcc 910 hsa-miR-3130-3p MIMAT0014994 GCUGCACCggagacuggguaa 911 hsa-miR-3131 MIMAT0014996 UCGAGGACugguggaagggccuu 912 hsa-miR-3132 MIMAT0014997 UGGGUAGAgaaggagcucagagga 913 hsa-miR-3133 MIMAT0014998 UAAAGAACucuuaaaacccaau 914 hsa-miR-378b MIMAT0014999 ACUGGACUuggaggcagaa 915 hsa-miR-3134 MIMAT0015000 UGAUGGAUaaaagacuacauauu 916 hsa-miR-3135 MIMAT0015001 UGCCUAGGcugagacugcagug 917 hsa-miR-466 MIMAT0015002 AUACACAUacacgcaacacacau 918 hsa-miR-3136 MIMAT0015003 CUGACUGAauagguagggucauu 919 hsa-miR-544b MIMAT0015004 ACCUGAGGuugugcauuucuaa 920 hsa-miR-3137 MIMAT0015005 UCUGUAGCcugggagcaauggggu 921 hsa-miR-3138 MIMAT0015006 UGUGGACAgugagguagagggagu 922 hsa-miR-3139 MIMAT0015007 UAGGAGCUcaacagaugccuguu 923 hsa-miR-3140 MIMAT0015008 AGCUUUUGggaauucagguagu 924 hsa-miR-548t MIMAT0015009 CAAAAGUGaucgugguuuuug 925 hsa-miR-3141 MIMAT0015010 GAGGGCGGguggaggagga 926 hsa-miR-3142 MIMAT0015011 AAGGCCUUucugaaccuucaga 927 hsa-miR-3143 MIMAT0015012 AUAACAUUguaaagcgcuucuuucg 928 hsa-miR-548u MIMAT0015013 CAAAGACUgcaauuacuuuugcg 929 hsa-miR-3144-5p MIMAT0015014 AGGGGACCaaagagauauauag 930 hsa-miR-3144-3p MIMAT0015015 AUAUACCUguucggucucuuua 931 hsa-miR-3145 MIMAT0015016 AGAUAUUUugaguguuuggaauug 932 hsa-miR-1273c MIMAT0015017 GGCGACAAaacgagacccuguc 933 hsa-miR-3146 MIMAT0015018 CAUGCUAGgauagaaagaaugg 934 hsa-miR-3147 MIMAT0015019 GGUUGGGCagugaggaggguguga 935 hsa-miR-548v MIMAT0015020 AGCUACAGuuacuuuugcacca 936 hsa-miR-3148 MIMAT0015021 UGGAAAAAacuggugugugcuu 937 hsa-miR-3149 MIMAT0015022 UUUGUAUGgauauguguguguau 938 hsa-miR-3150 MIMAT0015023 CUGGGGAGauccucgagguugg 939 hsa-miR-3151 MIMAT0015024 GGUGGGGCaaugggaucaggu 940 hsa-miR-3152 MIMAT0015025 UGUGUUAGaauaggggcaauaa 941 hsa-miR-3153 MIMAT0015026 GGGGAAAGcgaguagggacauuu 942 hsa-miR-3074 MIMAT0015027 GAUAUCAGcucaguaggcaccg 943 hsa-miR-3154 MIMAT0015028 CAGAAGGGgaguugggagcaga 944 hsa-miR-3155 MIMAT0015029 CCAGGCUCugcagugggaacu 945 hsa-miR-3156 MIMAT0015030 AAAGAUCUggaagugggagaca 946 hsa-miR-3157 MIMAT0015031 UUCAGCCAggcuagugcagucu 947 hsa-miR-3158 MIMAT0015032 AAGGGCUUccucucugcaggac 948 hsa-miR-3159 MIMAT0015033 UAGGAUUAcaagugucggccac 949 hsa-miR-3160 MIMAT0015034 AGAGCUGAgacuagaaagccca 950 hsa-miR-3161 MIMAT0015035 CUGAUAAGaacagaggcccagau 951 hsa-miR-3162 MIMAT0015036 UUAGGGAGuagaaggguggggag 952 hsa-miR-3163 MIMAT0015037 UAUAAAAUgagggcaguaagac 953 hsa-miR-3164 MIMAT0015038 UGUGACUUuaagggaaauggcg 954 hsa-miR-3165 MIMAT0015039 AGGUGGAUgcaaugugaccuca 955 hsa-miR-3166 MIMAT0015040 CGCAGACAaugccuacuggccua 956 hsa-miR-1260b MIMAT0015041 AUCCCACCacugccaccau 957 hsa-miR-3167 MIMAT0015042 AGGAUUUCagaaauacuggugu 958 hsa-miR-3168 MIMAT0015043 GAGUUCUAcagucagac 959 hsa-miR-3169 MIMAT0015044 UAGGACUGugcuuggcacauag 960 hsa-miR-3170 MIMAT0015045 CUGGGGUUcugagacagacagu 961 hsa-miR-3171 MIMAT0015046 AGAUGUAUggaaucuguauauauc 962 hsa-miR-3172 MIMAT0015047 UGGGGUUUugcaguccuua 963 hsa-miR-3173 MIMAT0015048 AAAGGAGGaaauaggcaggcca 964 hsa-miR-1193 MIMAT0015049 GGGAUGGUagaccggugacgugc 965 hsa-miR-323b-5p MIMAT0001630 AGGUUGUCcguggugaguucgca 966 hsa-miR-323b-3p MIMAT0015050 CCCAAUACacggucgaccucuu 967 hsa-miR-3174 MIMAT0015051 UAGUGAGUuagagaugcagagcc 968 hsa-miR-3175 MIMAT0015052 CGGGGAGAgaacgcagugacgu 969 hsa-miR-3176 MIMAT0015053 ACUGGCCUgggacuaccgg 970 hsa-miR-3177 MIMAT0015054 UGCACGGCacuggggacacgu 971 hsa-miR-3178 MIMAT0015055 GGGGCGCGgccggaucg 972 hsa-miR-3179 MIMAT0015056 AGAAGGGGugaaauuuaaacgu 973 hsa-miR-3180-5p MIMAT0015057 CUUCCAGAcgcuccgccccacgucg 974 hsa-miR-3180-3p MIMAT0015058 UGGGGCGGagcuuccggaggcc 975 hsa-miR-548w MIMAT0015060 AAAAGUAAcugcgguuuuugccu 976 hsa-miR-3181 MIMAT0015061 AUCGGGCCcucggcgccgg 977 hsa-miR-3182 MIMAT0015062 GCUUCUGUaguguaguc 978 hsa-miR-3183 MIMAT0015063 GCCUCUCUcggagucgcucgga 979 hsa-miR-3184 MIMAT0015064 UGAGGGGCcucagaccgagcuuuu 980 hsa-miR-3185 MIMAT0015065 AGAAGAAGgcggucggucugcgg 981 hsa-miR-3065-5p MIMAT0015066 UCAACAAAaucacugaugcugga 982 hsa-miR-3065-3p MIMAT0015378 UCAGCACCaggauauuguuggag 983 hsa-miR-3186-5p MIMAT0015067 CAGGCGUCugucuacguggcuu 984 hsa-miR-3186-3p MIMAT0015068 UCACGCGGagagauggcuuug 985 hsa-miR-3187 MIMAT0015069 UUGGCCAUggggcugcgcgg 986 hsa-miR-3188 MIMAT0015070 AGAGGCUUugugcggauacgggg 987 hsa-miR-3189 MIMAT0015071 CCCUUGGGucugaugggguag 988 hsa-miR-320e MIMAT0015072 AAAGCUGGguugagaagg 989 hsa-miR-3190-5p MIMAT0015073 UGUGGAAGguagacggccagaga 990 hsa-miR-3190-3p MIMAT0015074 UGGAAGGUagacggccagagag 991 hsa-miR-3191 MIMAT0015075 UGGGGACGuagcuggccagacag 992 hsa-miR-3192 MIMAT0015076 UCUGGGAGguuguagcaguggaa 993 hsa-miR-3193 MIMAT0015077 UCCUGCGUaggaucugaggagu 994 hsa-miR-3194 MIMAT0015078 GGCCAGCCaccaggagggcug 995 hsa-miR-3195 MIMAT0015079 CGCGCCGGgcccggguu 996 hsa-miR-3196 MIMAT0015080 CGGGGCGGcaggggccuc 997 hsa-miR-548x MIMAT0015081 UAAAAACUgcaauuacuuuca 998 hsa-miR-3197 MIMAT0015082 GGAGGCGCaggcucggaaaggcg 999 hsa-miR-3198 MIMAT0015083 GUGGAGUCcuggggaauggaga 1000 hsa-miR-3199 MIMAT0015084 AGGGACUGccuuaggagaaaguu 1001 hsa-miR-3200 MIMAT0015085 CACCUUGCgcuacucaggucug 1002 hsa-miR-3201 MIMAT0015086 GGGAUAUGaagaaaaau 1003 hsa-miR-514b-5p MIMAT0015087 UUCUCAAGagggaggcaaucau 1004 hsa-miR-514b-3p MIMAT0015088 AUUGACACcucugugagugga 1005 hsa-miR-3202 MIMAT0015089 UGGAAGGGagaagagcuuuaau 1006 hsa-miR-1273d MIMAT0015090 GAACCCAUgagguugaggcugcagu 1007 hsa-miR-4295 MIMAT0016844 CAGUGCAAuguuuuccuu 1008 hsa-miR-4296 MIMAT0016845 AUGUGGGCucaggcuca 1009 hsa-miR-4297 MIMAT0016846 UGCCUUCCugucugug 1010 hsa-miR-378c MIMAT0016847 ACUGGACUuggagucagaagagugg 1011 hsa-miR-4293 MIMAT0016848 CAGCCUGAcaggaacag 1012 hsa-miR-4294 MIMAT0016849 GGGAGUCUacagcaggg 1013 hsa-miR-4301 MIMAT0016850 UCCCACUAcuucacuuguga 1014 hsa-miR-4299 MIMAT0016851 GCUGGUGAcaugagaggc 1015 hsa-miR-4298 MIMAT0016852 CUGGGACAggaggaggaggcag 1016 hsa-miR-4300 MIMAT0016853 UGGGAGCUggacuacuuc 1017 hsa-miR-4304 MIMAT0016854 CCGGCAUGuccagggca 1018 hsa-miR-4302 MIMAT0016855 CCAGUGUGgcucagcgag 1019 hsa-miR-4303 MIMAT0016856 UUCUGAGCugaggacag 1020 hsa-miR-4305 MIMAT0016857 CCUAGACAccuccaguuc 1021 hsa-miR-4306 MIMAT0016858 UGGAGAGAaaggcagua 1022 hsa-miR-4309 MIMAT0016859 CUGGAGUCuaggauucca 1023 hsa-miR-4307 MIMAT0016860 AAUGUUUUuuccuguuucc 1024 hsa-miR-4308 MIMAT0016861 UCCCUGGAguuucuucuu 1025 hsa-miR-4310 MIMAT0016862 GCAGCAUUcauguccc 1026 hsa-miR-4311 MIMAT0016863 GAAAGAGAgcugagugug 1027 hsa-miR-4312 MIMAT0016864 GGCCUUGUuccugucccca 1028 hsa-miR-4313 MIMAT0016865 AGCCCCCUggccccaaaccc 1029 hsa-miR-4315 MIMAT0016866 CCGCUUUCugagcuggac 1030 hsa-miR-4316 MIMAT0016867 GGUGAGGCuagcuggug 1031 hsa-miR-4314 MIMAT0016868 CUCUGGGAaaugggacag 1032 hsa-miR-4318 MIMAT0016869 CACUGUGGguacaugcu 1033 hsa-miR-4319 MIMAT0016870 UCCCUGAGcaaagccac 1034 hsa-miR-4320 MIMAT0016871 GGGAUUCUguagcuuccu 1035 hsa-miR-4317 MIMAT0016872 ACAUUGCCagggaguuu 1036 hsa-miR-4322 MIMAT0016873 CUGUGGGCucagcgcgugggg 1037 hsa-miR-4321 MIMAT0016874 UUAGCGGUggaccgcccugcg 1038 hsa-miR-4323 MIMAT0016875 CAGCCCCAcagccucaga 1039 hsa-miR-4324 MIMAT0016876 CCCUGAGAcccuaaccuuaa 1040 hsa-miR-4256 MIMAT0016877 AUCUGACCugaugaaggu 1041 hsa-miR-4257 MIMAT0016878 CCAGAGGUggggacugag 1042 hsa-miR-4258 MIMAT0016879 CCCCGCCAccgccuugg 1043 hsa-miR-4259 MIMAT0016880 CAGUUGGGucuaggggucagga 1044 hsa-miR-4260 MIMAT0016881 CUUGGGGCauggaguccca 1045 hsa-miR-4253 MIMAT0016882 AGGGCAUGuccagggggu 1046 hsa-miR-4251 MIMAT0016883 CCUGAGAAaagggccaa 1047 hsa-miR-4254 MIMAT0016884 GCCUGGAGcuacuccaccaucuc 1048 hsa-miR-4255 MIMAT0016885 CAGUGUUCagagaugga 1049 hsa-miR-4252 MIMAT0016886 GGCCACUGagucagcacca 1050 hsa-miR-4325 MIMAT0016887 UUGCACUUgucucaguga 1051 hsa-miR-4326 MIMAT0016888 UGUUCCUCugucucccagac 1052 hsa-miR-4327 MIMAT0016889 GGCUUGCAugggggacugg 1053 hsa-miR-4261 MIMAT0016890 AGGAAACAgggaccca 1054 hsa-miR-4265 MIMAT0016891 CUGUGGGCucagcucuggg 1055 hsa-miR-4266 MIMAT0016892 CUAGGAGGccuuggcc 1056 hsa-miR-4267 MIMAT0016893 UCCAGCUCgguggcac 1057 hsa-miR-4262 MIMAT0016894 GACAUUCAgacuaccug 1058 hsa-miR-2355 MIMAT0016895 AUCCCCAGauacaauggacaa 1059 hsa-miR-4268 MIMAT0016896 GGCUCCUCcucucaggaugug 1060 hsa-miR-4269 MIMAT0016897 GCAGGCACagacagcccuggc 1061 hsa-miR-4263 MIMAT0016898 AUUCUAAGugccuuggcc 1062 hsa-miR-4264 MIMAT0016899 ACUCAGUCauggucauu 1063 hsa-miR-4270 MIMAT0016900 UCAGGGAGucaggggagggc 1064 hsa-miR-4271 MIMAT0016901 GGGGGAAGaaaaggugggg 1065 hsa-miR-4272 MIMAT0016902 CAUUCAACuagugauugu 1066 hsa-miR-4273 MIMAT0016903 GUGUUCUCugauggacag 1067 hsa-miR-4276 MIMAT0016904 CUCAGUGAcucaugugc 1068 hsa-miR-4275 MIMAT0016905 CCAAUUACcacuucuuu 1069 hsa-miR-4274 MIMAT0016906 CAGCAGUCccucccccug 1070 hsa-miR-4281 MIMAT0016907 GGGUCCCGgggagggggg 1071 hsa-miR-4277 MIMAT0016908 GCAGUUCUgagcacaguacac 1072 hsa-miR-4279 MIMAT0016909 CUCUCCUCccggcuuc 1073 hsa-miR-4278 MIMAT0016910 CUAGGGGGuuugcccuug 1074 hsa-miR-4280 MIMAT0016911 GAGUGUAGuucugagcagagc 1075 hsa-miR-4282 MIMAT0016912 UAAAAUUUgcauccagga 1076 hsa-miR-4285 MIMAT0016913 GCGGCGAGuccgacucau 1077 hsa-miR-4283 MIMAT0016914 UGGGGCUCagcgaguuu 1078 hsa-miR-4284 MIMAT0016915 GGGCUCACaucaccccau 1079 hsa-miR-4286 MIMAT0016916 ACCCCACUccugguacc 1080 hsa-miR-4287 MIMAT0016917 UCUCCCUUgagggcacuuu 1081 hsa-miR-4288 MIMAT0016918 UUGUCUGCugaguuucc 1082 hsa-miR-4292 MIMAT0016919 CCCCUGGGccggccuugg 1083 hsa-miR-4289 MIMAT0016920 GCAUUGUGcagggcuauca 1084 hsa-miR-4290 MIMAT0016921 UGCCCUCCuuucuucccuc 1085 hsa-miR-4291 MIMAT0016922 UUCAGCAGgaacagcu 1086 hsa-miR-4329 MIMAT0016923 CCUGAGACccuaguuccac 1087 hsa-miR-4330 MIMAT0016924 CCUCAGAUcagagccuugc 1088 hsa-miR-500b MIMAT0016925 AAUCCUUGcuaccugggu 1089 hsa-miR-4328 MIMAT0016926 CCAGUUUUcccaggauu 1090

Example 1 Inhibition of VAMP3 Expression by Single Stranded miR-124 Analogs

RT-qPCR Assays—

HCT-116 cells were cultured in McCoy's 5A Medium (Mediatech Inc.) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. These cells were plated in 96-well culture plates at a density of 6000 cells/well 24 hours prior to transfection.

Transfection was carried out using Opti-MEM I Reduced Serum Media (Gibco) and Lipofectamine RNAiMax (Invitrogen) with a final miRNA concentration of 10 nM for the data in FIGS. 1 and 2, and ranging from 30 nM down to 0.01 nM along a 12-point titration curve for the data in FIG. 3.

24 hours after transfection, cells were washed with phosphate-buffered saline and processed using the TaqMan® Gene Expression Cells-to-CT™ Kit (Applied Biosystems/Ambion) to extract RNA, synthesize cDNA, and perform RT-qPCR using a VAMP3-specific probe (Applied Biosystems) on an ABI Prism 7900HT Sequence Detector.

Reverse transcription conditions were as follows: 60 minutes at 37° C., followed by 5 minutes at 95° C. RT-qPCR conditions were as follows: 2 minutes at 50° C., 10 minutes at 95° C., followed by 40 cycles of 15 seconds at 95° C. and 1 minute at 60° C. GUSB mRNA levels were used for data normalization. Knockdown of VAMP3 was calculated as the two-fold change in VAMP3 cDNA measured in experimentally-treated cells relative to the VAMP3 cDNA measured in non-targeting control-treated cells.

Reporter Assays—

HCT-116 cells were cultured in McCoy's 5A Medium (Mediatech Inc.) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. These cells were plated in 96-well culture plates at a density of 25,000 cells/well 24 hours prior to transfection.

Transfection was carried out using Opti-MEM I Reduced Serum Media (Gibco) and Lipofectamine 2000 (Invitrogen) with a final miRNA concentration of 10 nM for the data in FIGS. 4 and 5, and ranging from 30 nM down to 0.01 nM along a 6-point titration curve for the data in FIG. 6. miRNAs were co-transfected with siCHECK2 vectors (Genscript) containing cloned target inserts consisting of a tandem repeat of a seed match to miR-124 (2×; FIG. 6A) or a full-length match to miR-124 (2×FL; FIG. 6B).

Twenty-four hours after transfection, transfection medium was replaced with fresh growth medium. Forty-eight hours after transfection, cells were lysed and both Firefly- and Renilla-Luciferase activity were measured using the Dual-Glo™ Luciferase Assay System (Promega) on a Wallac EnVision 2103 Multilabel Reader (PerkinElmer). Firefly-Luciferase activity was used to normalize Renilla-Luciferase activity, and the final data was calculated as two-fold change of the Renilla-Luciferase signal in experimentally-treated cells relative to non-targeting control-treated cells.

Oligonucleotide Synthesis—

Oligonucleotides were synthesized using protocols well known in the art (solid phase synthesis) using commercially available phosphoramidites, then purified by reversed phase solid phase extraction (SPE). The C3 (C₃₃H₄₃N₂O₅P) and C6 (C₃₆H₄₉N₂O₅P) phosphoramidites were purchased from ChemGenes.

Briefly, the single strand oligonucleotides were synthesized using phosphoramidite chemistry on an automated solid-phase synthesizer, using procedures as are generally known in the art (see, for example, U.S. application Ser. No. 12/064,014, published as US 20090176725). A synthesis column was packed with solid support derivatized with the first nucleoside residue (natural or chemically modified). Synthesis was initiated by detritylation of the acid labile 5′-O-dimethoxytrityl group to release the 5′-hydroxyl. A suitably protected phosphoramidite and a suitable activator in acetonitrile were delivered simultaneously to the synthesis column resulting in coupling of the amidite to the 5′-hydroxyl. The column was then washed with a solvent, such as acetonitrile. An oxidizing solution, such as an iodine solution was pumped through the column to oxidize the phosphite triester linkage P(III) to its phosphotriester P(V) analog. Unreacted 5′-hydroxyl groups were capped using reagents such as acetic anhydride in the presence of 2,6-lutidine and N-methylimidazole. The elongation cycle was resumed with the detritylation step for the next phosphoramidite incorporation. This process was repeated until the desired sequence was synthesized. The synthesis concluded with the final 5′-terminus protecting group (trityl or 5′-O-dimethoxytrityl).

Upon completion of the synthesis, the solid-support and associated oligonucleotide were dried under argon pressure or vacuum. Aqueous base was added and the mixture was heated to effect cleavage of the succinyl linkage, removal of the cyanoethyl phosphate protecting group, and deprotection of the exocyclic amine protection.

The following process was performed on single strands that do not contain ribonucleotides. After treating the solid support with the aqueous base, the mixture was filtered to separate the solid support from the deprotected crude synthesis material. The solid support was then rinsed with DMSO, which is combined with the filtrate. The resultant basic solution allows for retention of the 5′-O-dimethoxytrityl group to remain on the 5′ terminal position (trityl-on).

For single strands that contain ribonucleotides, the following process was performed. After treating the solid support with the aqueous base, the mixture was filtered to separate the solid support from the deprotected crude synthesis material. The solid support was then rinsed with dimethylsulfoxide (DMSO), which was combined with the filtrate. Fluoride reagent, such as triethylamine trihydrofluoride, was added to the mixture, and the solution was heated. The reaction was quenched with suitable buffer to provide a solution of crude single strand with the 5′-O-dimethoxytrityl group on the final 5′ terminal position.

The trityl-on solution of each crude single strand was purified using chromatographic purification, such as SPE RPC purification. The hydrophobic nature of the trityl group permits stronger retention of the desired full-length oligo than the non-tritylated truncated failure sequences. The failure sequences were selectively washed from the resin with a suitable solvent, such as low percent acetonitrile. Retained oligonucleotides were then detritylated on-column with trifluoroacetic acid to remove the acid-labile trityl group. Residual acid was washed from the column, a salt exchange was performed, and a final desalting of the material commenced. The full-length oligo was recovered in a purified form with an aqueous-organic solvent. The final product was then analyzed for purity (HPLC), identity (Maldi-TOF MS), and yield (UV A₂₆₀). The oligos were dried via lyophilization or vacuum condensation.

Results—

The ability of single-stranded miR-124 analogs to inhibit expression of a known target, VAMP3, was tested, wherein the miR-124 analogs comprise either a C3 spacer substituted for one nucleotide, or a C6 spacer substituted for two nucleotides, at various positions along the strand.

The passenger strand sequence of the miR-124 used in this study is 5′-GCAUUCACCGCGUGCCUUAAAU-3′ (SEQ ID NO: 1091), and the guide strand sequence is 5′-UUAAGGCACGCGGUGAAUGCCA-3′ (SEQ ID NO: 1092). The miR-124 analogs tested, as well as control molecules, are described in Table 2 and below.

TABLE 2 Name Sequence (5′ → 3′) * GIP (guide) UUAAGGCACGCGGUGAAUGCCA (SEQ ID NO: 1092) (passenger) GCAUUCACCGCGUGCCUUAAAU (SEQ ID NO: 1091) 21-8p-c3spacer-20 (guide) UAAGGCACGCGGUGAAUGC(C3-spacer)A (SEQ ID NO: 1093) 21-8p-c3spacer-19 (guide) UAAGGCACGCGGUGAAUG(C3-spacer)CA (SEQ ID NO: 1094) (FIG. 1, 3) c3pos19spacer (FIG. 2) c3pos19 (FIG. 4) 21-8p-c3spacer-18 (guide) UAAGGCACGCGGUGAAU(C3-spacer)C CA (SEQ ID NO: 1095) 21-8p-c3spacer-17 (guide) UAAGGCACGCGGUGAA(C3-spacer)GC CA (SEQ ID NO: 1096) 21-8p-c3spacer-16 (guide) UAAGGCACGCGGUGA(C3-spacer)UGC CA (SEQ ID NO: 1097) 21-8p-c3spacer-15 (guide) UAAGGCACGCGGUG(C3-spacer)AUGC CA (SEQ ID NO: 1098) (FIG. 1, 3) c3pos15spacer (FIG. 2) 21-8p-c3spacer-14 (guide) UAAGGCACGCGGU(C3-spacer)AAUGC CA (SEQ ID NO: 1099) (FIG. 1, 3) c3pos14 (FIG. 4) 21-8p-c3spacer-13 (guide) UAAGGCACGCGG(C3-spacer)GAAUGC CA (SEQ ID NO: 1100) 21-8p-c3spacer-12 (guide) UAAGGCACGCG(C3-spacer)UGAAUGC CA (SEQ ID NO: 1101) 21-8p-c3spacer-11 (guide) UAAGGCACGC(C3-spacer)GUGAAUGC CA (SEQ ID NO: 1102) 21-8p-c3spacer-10 (guide) UAAGGCACG(C3-spacer)GGUGAAUGC CA (SEQ ID NO: 1103) 21-8p-c3spacer-9 (guide) UAAGGCAC(C3-spacer)CGGUGAAUGC CA (SEQ ID NO: 1104) 21-8p-c3spacer-8 (guide) UAAGGCA(C3-spacer)GCGGUGAAUGC CA (SEQ ID NO: 1105) 21-8p-c3spacer-7 (guide) UAAGGC(C3-spacer)CGCGGUGAAUGC CA (SEQ ID NO: 1106) 21-8p-c3spacer-6 (guide) UAAGG(C3-spacer)ACGCGGUGAAUGC CA (SEQ ID NO: 1107) 21-8p-c3spacer-5 (guide) UAAG(C3-spacer)CACGCGGUGAAUGC CA (SEQ ID NO: 1108) 21-8p-c3spacer-4 (guide) UAA(C3-spacer)GCACGCGGUGAAUGC CA (SEQ ID NO: 1109) 21-8p-c3spacer-3 (guide) UA(C3-spacer)GGCACGCGGUGAAUGC CA (SEQ ID NO: 1110) 21-8p-c3spacer-2 (guide) U(C3-spacer)AGGCACGCGGUGAAUGC CA (SEQ ID NO: 1111) 21-8p-c6spacerdel2-19 (guide) UAAGGCACGCGGUGAAUG(C6-spacer)A (SEQ ID NO: 1112) 21-8p-c6spacerdel2-18 (guide) UAAGGCACGCGGUGAAU(C6-spacer)CA (SEQ ID NO: 1113) 21-8p-c6spacerdel2-17 (guide) UAAGGCACGCGGUGAA(C6-spacer)C CA (SEQ ID NO: 1114) 21-8p-c6spacerdel2-16 (guide) UAAGGCACGCGGUGA(C6-spacer)GC CA (SEQ ID NO: 1115) 21-8p-c6spacerdel2-15 (guide) UAAGGCACGCGGUG(C6-spacer)UGC CA (SEQ ID NO: 1116) (FIG. 1, 3) c6del2po s15 spacer (FIG. 2) 21-8p-c6spacerdel2-14 (guide) UAAGGCACGCGGU(C6-spacer)AUGC CA (SEQ ID NO: 1117) 21-8p-c6spacerdel2-13 (guide) UAAGGCACGCGG(C6-spacer)AAUGC CA (SEQ ID NO: 1118) 21-8p-c6spacerdel2-12 (guide) UAAGGCACGCG(C6-spacer)GAAUGC CA (SEQ ID NO: 1119) 21-8p-c6 spacerdel2-11 (guide) UAAGGCACGC(C6-spacer)UGAAUGC CA (SEQ ID NO: 1120) 21-8p-c6spacerdel2-10 (guide) UAAGGCACG(C6-spacer)GUGAAUGC CA (SEQ ID NO: 1121) 21-8p-c6spacerdel2-9 (guide) UAAGGCAC(C6-spacer)GGUGAAUGC CA (SEQ ID NO: 1122) 21-8p-c6spacerdel2-8 (guide) UAAGGCA(C6-spacer)CGGUGAAUGC CA (SEQ ID NO: 1123) 21-8p-c6spacerdel2-7 (guide) UAAGGC(C6-spacer)GCGGUGAAUGC CA (SEQ ID NO: 1124) UC3 (passenger) B gUaUgaCCgaCUaCgCgUatt B  (SEQ ID NO: 1125) (guide) UACG C G U AG UC GG UC A U A C UU (SEQ ID NO: 1126) miR-124 (FIG. 1) (guide) UUAAGGCACGCGGUGAAUGCCA (SEQ ID NO: 1127) pG (FIG. 2) 124(21)-8p-16rrr (guide) UAAGGCACGCGGUGAAUGC CA (SEQ ID NO: 1128) 124(21)-8p (FIG. 1) (guide) UAAGGCACGCGGUGAAUGC CA (SEQ ID NO: 1129) G-all-Fluoro (FIG. 2) pG-Fluoro (FIG. 4) GAPDH (guide) AAGUU G UC A U GGA U GA CCU UU (SEQ ID NO: 1131) (passenger) B aggUCaUCCaUgaCaaCUUtt B (SEQ ID NO: 1130) Renilla (guide) UAGUUGCGGACAAUCUGGAtt (SEQ ID NO: 1133) (passenger) UCCAGAUUGUCCGCAACUAtt (SEQ ID NO: 1132) C6delpos15spacer/P (guide) UAAGGCACGCGGUG(C6-spacer)UGC CA (SEQ ID NO: 1116) (passenger) GCAUUCACCGCGUGCCUUAAAU (SEQ ID NO: 1091) pG-Fluoro/Pshort (guide) UAAGGCACGCGGUGAAUGC CA (SEQ ID NO: 1129) (passenger) GCAUUCACCGCGUGCCUUAAU (SEQ ID NO: 1134) * A, U, C, and G = 2′-deoxy-2′-fluoro A, U, C, and G A, U, C, and G = 2′-O-methyl (2′-OMe) A, U, C, and G a, g, c and u = deoxy A, U, C,and G t = thymidine A, C, G, and U = ribose A, C, G or U B = inverted abasic

All of the single-stranded molecules in Table 2 contain a 5′ phosphate cap.

“G/P” represents double-stranded miR-124, wherein the duplex has two nucleotide overhangs on the 3′ ends of the passenger and guide strands. The guide strand of the G/P duplex is 22 nucleotides in length.

SEQ ID NOs: 1093-1124 represent analogs of the single-stranded miR-124 guide strand. Each of these molecules are a 21-nucleotide version of the miR-124 guide strand that is present in the G/P duplex, missing the 5′-uracil nucleotide that is present in the 22-nucleotide G/P miR-124 guide strand. All of the nucleotides in these 21-mer analogs, with the exception of the 3′ adenosine, and the adjacent cytosine (if present), are chemically modified on the ribose moiety with 2′-fluoro (depicted as italicized nucleotides in Table 2). The 3′ adenosine, and the adjacent cytosine (if present), are chemically modified on the ribose moiety with 2′-O-methyl (depicted as underlined nucleotides in Table 2). Finally, the 21-mer analogs of the miR-124 guide strand contain either a C3-spacer substituted for one nucleotide (the “c3spacer” analogs) or a C6-spacer substituted for two nucleotides (the “c6spacerdel2” analogs) at the various denoted positions along the strand. For example “21-8p-c3spacer-20” represents a 21-mer miR-124 guide strand analog containing an ethylene glycol spacer in the place of the nucleotide at position 20 within the 21-nucleotide miR-124 guide strand, linking the nucleotides at position 19 and position 21. As another example, the analog labeled “21-8p-c6spacerdel2-19” represents a 21-mer miR-124 guide strand analog containing a hexane spacer in the place of the nucleotides at positions 19 and 20 within the 21-nucleotide miR-124 guide strand, linking the nucleotides at positions 18 and 21. Some of the 21-nucleotide miR-124 guide strand analogs have different names in accompanying Figures, as noted in Table 2. For example, the 21-mer miR-124 guide strand analog represented by SEQ ID NO: 1116 is called “21-8p-c6spacerdel2-15” in FIGS. 1 and 3 and “c6del2pos15spacer” in FIG. 2.

“UC3” represents a non-targeting, chemically-modified duplex.

“124(21)-8p-16rrr” represents an analog of the 21-nucleotide version of the miR-124 guide strand. This molecule does not contain an internal spacer. All of the nucleotides are modified with 2′-fluoro, with the exception of nucleotides 16-18, which are RNA, and nucleotides 21 and 22, which are modified with 2′-O-methyl.

“124(21)-8p” represents a 21-nucleotide version of the miR-124 guide, wherein nucleotides 1-20 are modified with 2′-fluoro and nucleotides 20 and 21 are modified with 2′-O-methyl.

“124(21)-8p” is the name of this analog in FIG. 1; “G-all Fluoro” is the name of this analog in FIG. 2; and, “pG-Fluoro” is the name of this analog in FIG. 4.

“miR-124” is the single-stranded guide strand of the G/P duplex. It is 22 nucleotides in length and unmodified.

“C6delpos15spacer/P” represents a double-stranded miR-124 duplex, wherein the guide strand has the structure of “21-8p-c6spacerdel2-15” (SEQ ID NO: 1116), and the passenger strand is the 22-nucleotide miR-124 passenger strand (SEQ ID NO: 1091).

FIGS. 1 and 2 show the degree of inhibition of VAMP3 target expression by the single-stranded miR-124 analogs described in Table 2 using the RT-qPCR assay described above. FIG. 1 shows the degree of inhibition by the single-stranded miR-124 analogs containing a C3 spacer. FIG. 2 shows the degree of inhibition by the single-stranded miR-124 analogs containing a C6 spacer. The longer bars in each figure indicate greater knockdown of VAMP3. The duplicate bars indicate biological replicates, each representing data from a separate well of cells (on two separate plates) transfected with the indicated nucleic acid molecules. The spacer appears to be most well-tolerated at position 19, and in the vicinity of position 15, of the miR-124 analogs.

The graph in FIG. 3 depicts the dose-dependent response of VAMP3 expression to a subset of the analogs tested in FIGS. 1 and 2 (see Table 2 for sequences). VAMP3 expression is depicted along the y-axis, thus data points with lower values along this axis indicate greater VAMP3 expression knockdown. The dose of the miR-124 analog tested is depicted along the x-axis, ranging from the lowest doses on the left to the highest doses on the right. Although the double stranded versions (G/P and c6del2pos15spacer/P) are more potent than the single-stranded analogs, it is worth noting that the single-stranded “G-all Fluoro” analog (no internal spacer, nucleotides 1-20 are 2′-fluoro, nucleotides 20 and 21 are 2′-O-methyl) behaves almost identically to comparable single-stranded analogs with a C3 spacer replacing position 15 (c3pos15spacer) or position 19 (c3pos19spacer).

FIGS. 4 and 5 show data from a screen of the same single-stranded miR-124 analogs tested in FIGS. 1 and 2, measuring knockdown of a co-transfected luciferase reporter that carries two target sites matching the seed region of miR-124. Thus, the data from this assay is a representation of the miRNA activity of the tested analogs. FIG. 4 shows the degree of inhibition by the single-stranded miR-124 analogs that contain a C3 spacer. FIG. 5 shows the degree of inhibition by the single-stranded miR-124 analogs that contain a C6 spacer. The duplicate bars indicate biological replicates, each representing data from a separate well of cells (on two separate plates) transfected with the indicated molecules. Again, the longer bars indicate greater inhibition, showing that the analogs that contain a spacer at position 19, or in the vicinity of position 15, have the greatest knockdown activity.

The graphs in FIG. 6 depict the dose-dependent response of target expression inhibition of two different luciferase reporters to a subset of the analogs tested in FIG. 3. In FIG. 6A, the inhibition activity shown is against a luciferase reporter with two matches to the miR-124 seed region. Thus, this is a representation of the miRNA activity of the tested analogs. In FIG. 6B, the inhibition activity shown is against a luciferase reporter with two full-length matches to miR-124 and, thus, represents the siRNA activity of the tested analogs. In both A and B, the G/P curves represent activity by a miR-124 duplex made up entirely of RNA. The pG-Fluoro/Pshort curves represent activity by a guide strand that is predominantly modified with 2′-fluoro nucleotides duplexed to an all-RNA passenger strand. The pG-Fluoro curves represent the activity of a single-stranded miR-124 guide strand analog that is predominantly modified with 2′-fluoro nucleotides. The c3pos14 and c3pos19 curves represent the activity of analogs of pG-Fluoro, only differing from pG-Fluoro by containing a 3-carbon spacer (C3-spacer) substituted for position 14 (“c3pos14”) or position 19 (“c3pos19”). All of the single-stranded analogs show less potency than either duplexes against the reporter with only seed matches, but they are effectively equivalent to each other across all concentrations and show similar activity to the duplexes at the highest concentration (FIG. 6A). Against the reporter with full-length matches, the all-RNA duplex (“G/P”) was still the strongest performer, but the spacer-containing single-stranded analogs had activity as strong as or stronger than the duplex with the 2′-fluoro guide strand (“pG-Fluoro/Pshort”) and the single-strand (“pG-Fluoro”).

Example 2 Single-Strand RNAi Knockdown of ApoB mRNA

RT-qPCR Assays (Primary Screens and Dose-Response Curves)—

Hepa1-6 cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum, 1% penicillin-steptomycin, and 1% sodium bicarbonate. These cells were plated in a 96-well culture plates at a density of 3000 cells/well 24 hours prior to transfection.

Transfections were performed using Opti-MEM I Reduced Serum Media and Lipofectamine RNAiMAX per the manufacturer's directions. Final single-stranded siRNA concentrations were 100 nM and 10 nM.

Twenty-four hours post-transfection, cells were washed with phosphate-buffered saline and processed using the TaqMan Gene Expression Cells-to-CT™ Kit, per manufacturer's instructions, to extract RNA, synthesize cDNA, and perform RT-qPCR using an ApoB specific Taqman primer/probe set on an ABI Prism 7900HT Sequence Detector.

Reverse transcription conditions were as follows: 60 minutes at 37° C. followed by 5 minutes at 95° C. RT-qPCR conditions were as follows: 2 minutes at 50° C., 10 minutes at 95° C., followed by 40 cycles of 15 seconds at 95° C. and 1 minute at 60° C. GADPH mRNA levels were used for data normalization.

Knockdown of ApoB was calculated as the two-fold change in ApoB cDNA measured in experimentally-treated cells relative to the ApoB cDNA measured in non-targeting, control-treated cells.

Results—

The knockdown of ApoB mRNA was measured using single strand (guide strand) oligonucleotides with a C3 spacer incorporated at either position 15, 16, 17, 18, or 19 (relative to the 5′ of the oligo) at two different concentrations (100 nM and 10 nM). The results are shown in FIG. 7. All of the single strand molecules tested are composed of 2′-deoxy-2′-fluoro nucleotides at both pyrimidine and purine nucleotides and a 5′ phosphate. The two 3′ terminal nucleotides of each molecule are 2′-O-methyl nucleotides. Single strand molecule “485” (see FIG. 7; 5′-UUAAGAGAAGCCUUACUGGUU-3′ (SEQ ID NO: 1135)) is a 21-nucleotide molecule that does not contain a C3 spacer and targets ApoB mRNA at nucleotide position 485. A C3 spacer is incorporated into molecule 485 at positions 15 (“485 c3@pos15”; SEQ ID NO: 1136), 16 (“485 c3@pos16”; SEQ ID NO: 1137), 17 (“485 c3@pos17”; SEQ ID NO: 1138), 18 (“485 c3@pos18”; SEQ ID NO: 1139) or 19 (“485 c3@pos19”; SEQ ID NO: 1140) (i.e., the spacer takes the place of the indicated nucleotide of the 485 molecule). For example, signal strand molecule “485 c3@pos15” is represented by: 5′-UUAAGAGAAGCCUU(C3-spacer)CUGGUU-3′; SEQ ID NO: 1136). As shown in FIG. 7, inclusion of the C3 spacer at positions 18 or 19 is both well tolerated and improves mRNA knockdown at two different concentrations (100 nM and 10 nM). This data indicates that incorporation of a non-nucleotide C3 carbon spacer at the 3′ end of a single strand RNA interference oligonucleotide improves the potency of mRNA knockdown (FIG. 7).

To evaluate whether the incorporation of a C3 spacer in single strands was more broadly applicable, 30 different single strand sequences targeting ApoB, each with a C3 spacer at either position 18 (FIG. 8) or position 19 (FIG. 9), were evaluated at two concentrations (100 nM and 10 nM). In FIGS. 8 and 9, the single-stranded molecules are notated by the position within the ApoB mRNA which they target. All of the single-stranded molecules tested are composed of 2′-deoxy-2′-fluoro nucleotides at both pyrimidine and purine nucleotides and a 5′ phosphate. The two 3′ terminal nucleotides of each molecule are 2′-O-methyl nucleotides. The sequence identifiers (SEQ ID NOs:) of the single stranded RNAi molecules evaluated in FIGS. 8 and 9 are listed in Table 3.

TABLE 3 ApoB Target C3-position 18 C3-position 19 No spacer Region (FIGS. 8 and 10) (FIGS. 9 and 10) (FIG. 10) 19 SEQ ID NO: 1141 SEQ ID NO: 1170 SEQ ID NO: 1199 248 SEQ ID NO: 1142 SEQ ID NO: 1171 SEQ ID NO: 1200 397 SEQ ID NO: 1143 SEQ ID NO: 1172 SEQ ID NO: 1201 485 SEQ ID NO: 1139 SEQ ID NO: 1140 SEQ ID NO: 1135 601 SEQ ID NO: 1144 SEQ ID NO: 1173 SEQ ID NO: 1202 719 SEQ ID NO: 1145 SEQ ID NO: 1174 SEQ ID NO: 1203 780 SEQ ID NO: 1146 SEQ ID NO: 1175 SEQ ID NO: 1204 1124 SEQ ID NO: 1147 SEQ ID NO: 1176 SEQ ID NO: 1205 1445 SEQ ID NO: 1148 SEQ ID NO: 1177 SEQ ID NO: 1206 1446 SEQ ID NO: 1149 SEQ ID NO: 1178 SEQ ID NO: 1207 1611 SEQ ID NO: 1150 SEQ ID NO: 1179 SEQ ID NO: 1208 1983 SEQ ID NO: 1151 SEQ ID NO: 1180 SEQ ID NO: 1209 3214 SEQ ID NO: 1152 SEQ ID NO: 1181 SEQ ID NO: 1210 3614 SEQ ID NO: 1153 SEQ ID NO: 1182 SEQ ID NO: 1211 4542 SEQ ID NO: 1154 SEQ ID NO: 1183 SEQ ID NO: 1212 6548 SEQ ID NO: 1155 SEQ ID NO: 1184 SEQ ID NO: 1213 6930 SEQ ID NO: 1156 SEQ ID NO: 1185 SEQ ID NO: 1214 6981 SEQ ID NO: 1157 SEQ ID NO: 1186 SEQ ID NO: 1215 7044 SEQ ID NO: 1158 SEQ ID NO: 1187 SEQ ID NO: 1216 9414 SEQ ID NO: 1159 SEQ ID NO: 1188 SEQ ID NO: 1217 9514 SEQ ID NO: 1160 SEQ ID NO: 1189 SEQ ID NO: 1218 9621 SEQ ID NO: 1161 SEQ ID NO: 1190 SEQ ID NO: 1219 10162 SEQ ID NO: 1162 SEQ ID NO: 1191 SEQ ID NO: 1220 10167 SEQ ID NO: 1163 SEQ ID NO: 1192 SEQ ID NO: 1221 10168 SEQ ID NO: 1164 SEQ ID NO: 1193 SEQ ID NO: 1222 10219 SEQ ID NO: 1165 SEQ ID NO: 1194 SEQ ID NO: 1223 10455 SEQ ID NO: 1166 SEQ ID NO: 1195 SEQ ID NO: 1224 10517 SEQ ID NO: 1167 SEQ ID NO: 1196 SEQ ID NO: 1225 12673 SEQ ID NO: 1168 SEQ ID NO: 1197 SEQ ID NO: 1226 13666 SEQ ID NO: 1169 SEQ ID NO: 1198 SEQ ID NO: 1227

In FIGS. 8 and 9, the data was normalized to the corresponding single-stranded molecule without the C3 spacer. Knockdown amounts that are equivalent to the single-stranded controls (without C3 spacer) would be centered at 0, while positive values indicate that incorporation of the C3 spacer confers an improvement in mRNA knockdown. Negative values indicate a deleterious effect of C3 spacer inclusion. Note that due to experimental variation with in vitro assays, only values greater than +0.5 or less than −0.5 are considered significant. For example, inclusion of the C3 spacer in ApoB molecule 485 at position 18 does not have a significant improvement over the single strand control since the difference in knockdown shown in the FIG. 8 is less than 0.5. However, inclusion of the C3 spacer in the same single strand guide molecule at position 19 has a significant improvement in knockdown (see FIG. 9). Overall, inclusion of the C3 spacer at position 19 is preferred as incorporation at this position seems to improve the potency of mRNA knockdown for the majority of the 30 different sequences tested (73%).

In FIG. 10, ApoB mRNA knockdown at 100 nM concentration using single stranded molecules targeting each of the 30 different ApoB target sites tested in FIGS. 8 and 9 were compared—single strands without C3 spacer (“all-flu-p”), with C3 spacer at position 18 (“all-flu-c3-18-p”), and with C3 spacer at position 19 (“all-flu-c3-19-p”). All of the single-stranded molecules tested are composed of 2′-deoxy-2′-fluoro nucleotides at both pyrimidine and purine nucleotides and a 5′ phosphate. The two 3′ terminal nucleotides of each molecule are 2′-O-methyl nucleotides. The sequence identifiers (SEQ ID NOs:) of the single stranded RNAi molecules evaluated in FIG. 10 are listed in Table 3. FIG. 10 demonstrates the range in overall efficacy of mRNA knockdown for different single-stranded sequences. For example, single strand molecules targeting ApoB target site 485 is maximally effective, while others like those targeting ApoB target site 780 or 10219 have limited mRNA knockdown. For each of the 30 different sequences, the mRNA knockdown shown in FIG. 10 was normalized to the corresponding strands which do not contain the C3 spacer (“all-flu-p”). 

What is claimed:
 1. A single-stranded RNA molecule that mediates RNA interference against a target RNA, wherein said single-stranded RNA molecule comprises one or more internal, non-nucleotide spacer, wherein the non-nucleotide spacer comprises a C3-C6 alkyl.
 2. The molecule of claim 1, wherein the total number of nucleotides in the single-stranded RNA molecule is 8 to 26 nucleotides.
 3. The molecule of claim 1, wherein the target RNA comprises a target site that is within an untranslated region of the target RNA.
 4. The molecule of claim 3, wherein the single-stranded RNA molecule comprises at least 20 nucleotides that can base pair with the target site as the whole or as a part of a seed-targeted sequence of a naturally-occurring, endogenous miRNA nucleotide sequence.
 5. The molecule of claim 4, wherein the single-stranded RNA molecule is a single-stranded siRNA or the guide (antisense) strand of a duplex siRNA.
 6. The molecule of claim 4, wherein nucleotides in the single-stranded RNA molecule are at least 50% homologous to the naturally-occurring, endogenous miRNA nucleotide sequence.
 7. The molecule of claim 1, wherein the target RNA comprises a target site that is within a gene coding region of the target RNA.
 8. The molecule of claim 1, wherein nucleotides in the single-stranded RNA molecule are at least 90% complementary to a target site comprised by the target RNA.
 9. The molecule of claim 1, wherein at least one nucleotide of the single-stranded RNA molecule has a modified sugar.
 10. The molecule of claim 1, wherein at least one nucleotide of the single-stranded RNA molecule has a modified internucleotide linkage.
 11. The molecule of claim 1, having a terminal cap at the 5′-end, the 3′-end, or both the 5′- and 3′-ends.
 12. The molecule of claim 1, having a terminal group at the 5′-end, the 3′-end, or both the 5′- and 3′-ends.
 13. The molecule of claim 12, wherein the terminal group is a ligand.
 14. The molecule of claim 13, wherein the ligand is a ligand for a cellular receptor.
 15. The molecule of claim 14, wherein the ligand is a carbohydrate.
 16. The molecule of claim 15, wherein the carbohydrate is an N-acetyl-D-galactosamine.
 17. A composition comprising the single-stranded RNA molecule of claim 1 and a pharmaceutically acceptable carrier.
 18. The composition of claim 17, further comprising a liposome, a hydrogel, a cyclodextrin, a biodegradable nanocapsule, a bioadhesive microsphere, or a proteinaceous vector.
 19. A method of reducing the expression of an endogenous RNA target gene in a cell, comprising contacting the cell with the composition of claim
 17. 20. The molecule of claim 1, wherein the single-stranded RNA molecule comprises a nucleic acid portion comprising a first nucleotide portion (N1) and a second nucleotide portion (N2), wherein N1 comprises one nucleotide or a contiguous stretch of nucleotides and N2 comprises one nucleotide or a contiguous stretch of nucleotides, wherein the one or more internal, non-nucleotide spacer (S1) covalently links N1 and N2, wherein the single-stranded RNA molecule comprises the following structure: 5′ N1-S1-N2 3′.
 21. The molecule of claim 20, wherein N1 comprises 18 contiguous nucleotides, 19 contiguous nucleotides, or 20 contiguous nucleotides.
 22. The molecule of claim 20, wherein N2 comprises 2 contiguous nucleotides or 1 nucleotide. 